Small and long non-coding RNAs in cardiac homeostasis and regeneration

Cardiovascular diseases and in particular heart failure are major causes of morbidity and mortality in the Western world. Recently, the notion of promoting cardiac regeneration as a means to replace lost cardiomyocytes in the damaged heart has engendered considerable research interest. These studies envisage the utilization of both endogenous and exogenous cellular populations, which undergo highly specialized cell fate transitions to promote cardiomyocyte replenishment. Such transitions are under the control of regenerative gene regulatory networks, which are enacted by the integrated execution of specific transcriptional programs. In this context, it is emerging that the non-coding portion of the genome is dynamically transcribed generating thousands of regulatory small and long non-coding RNAs, which are central orchestrators of these networks. In this review, we discuss more particularly the biological roles of two classes of regulatory non-coding RNAs, i.e. microRNAs and long non-coding RNAs, with a particular emphasis on their known and putative roles in cardiac homeostasis and regeneration. Indeed, manipulating non-coding RNA-mediated regulatory networks could provide keys to unlock the dormant potential of the mammalian heart to regenerate. This should ultimately improve the effectiveness of current regenerative strategies and discover new avenues for repair. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.

Validation française de l'échelle d'expérience temporelle du plaisir [Validation of the Temporal Experience of Pleasure Scale (TEPS) in a French-speaking environment.]

INTRODUCTION: Anhedonia is defined as a diminished capacity to experience pleasant emotion and is commonly included among the negative symptoms of schizophrenia. However, if patients report experiencing a lower level of pleasure than controls, they report experiencing as much pleasure as controls with online measurements of emotion. OBJECTIVE: The Temporal Experience of Pleasure Scale (TEPS) measures pleasure experienced in the moment and in anticipation of future activities. The TEPS is an 18-item self-report measurement of anticipatory (10 items) and consummatory (eight items) pleasure. The goal of this paper is to assess the psychometric characteristics of the French translation of this scale. METHODS: A control sample was composed of 60 women and 22 men, with a mean age of 38.1 years (S.D.: 10.8). Thirty-six were without qualification and 46 with qualified professional diploma. A sample of 21 patients meeting DSM IV-TR criteria for schizophrenia was recruited among the community psychiatry service of the department of psychiatry in Lausanne. They were five women and 16 men; mean age was of 34.1 years (S.D.: 7.5). Ten obtained a professional qualification and 11 were without qualification. None worked in competitive employment. Their mean dose of chlorpromazine equivalent was 431mg (S.D.: 259). All patients were on atypical antipsychotics. The control sample fulfilled the TEPS and the Physical Anhedonia Scale (PAS). The patient sample fulfilled the TEPS and was independently rated on the Calgary Depression Scale and the Scale for Assessment of Negative Symptoms. For comparison with controls, patients were matched on age, sex and professional qualification. This required the supplementary recruitment of two control subjects. RESULTS: Results with the control sample indicate that the TEPS presents an acceptable internal validity with Crombach alphas of 0.84 for the total scale, 0.74 for the anticipatory pleasure scale and 0.79 for the consummatory pleasure scale. The confirmatory factor analysis indicated that the model is well adapted to our data (chi(2)/dl=1.333; df=134; p<0.0006; root mean square residual, RMSEA=0.064). External validity measured with the PAS showed R=-0.27 (p<0.05) for the consummatory scale and R=-0.26 for the total score. Comparisons between patients and matched controls indicated that patients were significantly lower than control on anticipatory pleasure (t=2.7, df(40), 2-tailed p=0.01; cohen's d=0.83) and on total score of the TEPS (t=2.8, df (40), 2-tailed p=0.01; cohen's d=0.87). The two samples did not differ on consummatory pleasure. The anticipatory pleasure factor and the total TEPS showed significant negative correlation with the SANS anhedonia, respectively R=-0.78 (p<0.01) for the anticipatory factor and R=-0.61 (p<0.01) for the total TEPS. There was also a negative correlation between the anticipatory factor and the SANS avolition of R=-0.50 (p<0.05). These correlations were maintained, with partial correlations controlling for depression and chlorpromazine equivalents. CONCLUSION: The results of this validation show that the French version of the TEPS has psychometric characteristics similar to the original version. These results highlight the discrepancy between results of direct or indirect report of experienced pleasure in patients with schizophrenia. Patients may have difficulties in anticipating the pleasure of future enjoyable activities, but not in experiencing pleasure once in an enjoyable activity. Medication and depression do not seems to modify our results, but this should be better controlled in a longitudinal study. The anticipatory versus consummatory pleasure distinction appears to be useful for the development of new psychosocial interventions, tailored to improve desire in patients suffering from schizophrenia. Major limitations of the study are the small size of patient sample and the under representation of men in the control sample.

Tandem use of solid-phase extraction and dispersive liquid-liquid microextraction for the determination of mononitrotoluenes in aquatic environment.

Solid-phase extraction (SPE) in tandem with dispersive liquid-liquid microextraction (DLLME) has been developed for the determination of mononitrotoluenes (MNTs) in several aquatic samples using gas chromatography-flame ionization (GC-FID) detection system. In the hyphenated SPE-DLLME, initially MNTs were extracted from a large volume of aqueous samples (100 mL) into a 500-mg octadecyl silane (C(18) ) sorbent. After the elution of analytes from the sorbent with acetonitrile, the obtained solution was put under the DLLME procedure, so that the extra preconcentration factors could be achieved. The parameters influencing the extraction efficiency such as breakthrough volume, type and volume of the elution solvent (disperser solvent) and extracting solvent, as well as the salt addition, were studied and optimized. The calibration curves were linear in the range of 0.5-500 μg/L and the limit of detection for all analytes was found to be 0.2 μg/L. The relative standard deviations (for 0.75 μg/L of MNTs) without internal standard varied from 2.0 to 6.4% (n=5). The relative recoveries of the well, river and sea water samples, spiked at the concentration level of 0.75 μg/L of the analytes, were in the range of 85-118%.

Global mass wasting during the Middle Ordovician: Meteoritic trigger or plate-tectonic environment ?

Mass wasting at continental margins on a global scale during the Middle Ordovician has recently been related to high meteorite influx. Although a high meteorite influx during the Ordovician should not be neglected, we challenge the idea that mass wasting was mainly produced by meteorite impacts over a period of almost 10 Ma. Having strong arguments against the impact-related hypothesis, we propose an alternative explanation, which is based on a re-evaluation of the mass wasting sites, considering their plate-tectonic distribution and the global sea level curve. A striking and important feature is the distribution of most of the mass wasting sites along continental margins characterised by periods of magmatism, terrane accretion and continental or back-arc rifting, respectively, related to subduction of oceanic lithosphere. Such processes are commonly connected with seismic activity causing earthquakes, which can cause downslope movement of sediment and rock. Considering all that, it seems more likely that most of this mass wasting was triggered by earthquakes related to plate-tectonic processes, which caused destabilisation of continental margins resulting in megabreccias and debris flows. Moreover, the period of mass wasting coincides with sea level drops during global sea level lowstand. In some cases, sea level drops can release pore-water overpressure reducing sediment strength and hence promoting instability of sediment at continental margins. Reduced pore-water overpressure can also destabilise gas hydrate-bearing sediment, causing slope failure, and thus resulting in submarine mass wasting. Overall, the global mass wasting during the Middle Ordovician does not need meteoritic trigger. (C) 2010 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

BACKGROUND: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. RESULTS: We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. CONCLUSIONS: The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.

The adaptative function of melanin-based colour variants

Résumé : Les mécanismes de contrôle des couleurs mélaniques chez les vertébrés sont encore discutés parmi les biologistes de l'évolution. Une hypothèse récente affirme que les effets pléiotropies du système des mélanocortines expliquent l'association fréquente entre la coloration eumélanique noire (due à la déposition d'eumélanine) et de nombreux traits physiologiques et comportementaux. De nombreuses études suggèrent, en effet, que des niveaux plus élevés des mélanocortines induisent l'assombrissement des téguments eumélaniques et affectent d'autres traits phénotypiques simultanément. Cependant, il n'est pas encore établi si ce mécanisme de pléiotropie peut s'appliquer aux colorations dues à la déposition de phaeomélanine, une autre forme commune de mélanine. Les antagonistes des mélanocortines déclenchent le phaeomélanogenèse et bloquent l'effet des mélanocortines ou ont un effet pharmacologique opposé. Nous nous proposons donc d'évaluer l'hypothèse que les effets pléiotropes des antagonistes des mélanocortines génèrent des covariations entre la coloration phaeomélanique et des aspects de la qualité individuelle. Comme prédit par cette hypothèse, nous constatons chez la chouette effraie (Tyto alba) que les traits phénotypiques (résistance au stress oxydatif et aux parasites) corrèlent positivement au degré d'expression d'une couleur eumélanique mais négativement au degré d'expression d'une coloration phaeomélanique. Puis, nous montrons chez la chouette hulotte (Strix aluco) que les associations génétiques entre la coloration phaeomélanique et la physiologie (immunité et la régulation de l'homéostasie) confèrent des avantages aux individus de différentes couleurs dans différents environnements caractérisés par l'abondance de nourriture et le niveau d'exposition aux parasites. Ainsi, nos études soutiennent l'hypothèse que les effets pléiotropes des antagonistes des mélanocortines génèrent des covariations entre les traits mélaniques et divers aspects de la qualité individuelle. Finalement, nous montrons chez le faucon crécerelle (Falco Tinnunculus) que l'expression des ornements mélaniques est sensible à la qualité de l'environnement dans lequel les individus grandissent. Ceci suggère que les gènes codant pour les mélanocortines et leurs antagonistes pourraient induire une expression des traits mélaniques dépendante de la condition de l'individu, un pattern d'expression rarement observé pour des traits généralement sous fort contrôle génétique. Summary : The information content and control mechanisms of melanin-based colour signals in vertebrates are still debated among evolutionary biologists. A recent hypothesis contends that pleiotropic effects of the melanocortin system accounts for the frequent association between black eumelanic coloration and physiological and behavioural traits. Accordingly, empirical evidence suggests that higher levels of melanocortins concurrently promote darker eumelanic integuments and affect other phenotypic traits. However, whether this mechanism may apply to signals relying on phaeomelanin, another common form of melanin pigments, remains to be established. Melanocortin antagonists trigger phaeomelanogenesis and block the effect of melanocortins or result in the opposite pharmacological effect. Therefore, we tested the hypothesis that pleiotropic effects of melanocortin antagonists and inverse agonists account for covariations between phaeomelanin-based coloration and aspects of individual quality. As predicted, we found that phenotypic traits (resistance to oxidative stress and parasites) correlated positively with a eumelanic trait and negatively with a phaeomelanic trait in the barn owl (Tyto alba). Then, we showed in the tawny owl (Strix aluco) that genetic associations between phaeomelanin-based coloration and physiology (immunity and regulation of energy homeostasis) confer benefits to differently coloured individuals under different levels of food abundance and parasite exposure. Altogether, our studies support the hypothesis that pleiotropic effects of melanocortins antagonists can indeed account for covariations between phaeomelanin-based traits and aspects of individual quality. Eventually, we show in the Eurasian kestrel (Falco Tinnunculus) that expression of melanin-based ornaments is sensitive to the environment in which individuals grow. This suggests that genes coding for melanocortins and their antagonists can mediate the condition-dependent component of melanin-based traits.

Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

A tumor-specific cellular environment at the brain invasion border of adamantinomatous craniopharyngiomas.

Craniopharyngiomas (CP) are benign epithelial tumors of the sellar region and can be clinicopathologically distinguished into adamantinomatous (adaCP) and papillary (papCP) variants. Both subtypes are classified according to the World Health Organization grade I, but their irregular digitate brain infiltration makes any complete surgical resection difficult to obtain. Herein, we characterized the cellular interface between the tumor and the surrounding brain tissue in 48 CP (41 adaCP and seven papCP) compared to non-neuroepithelial tumors, i.e., 12 cavernous hemangiomas, 10 meningiomas, and 14 metastases using antibodies directed against glial fibrillary acid protein (GFAP), vimentin, nestin, microtubule-associated protein 2 (MAP2) splice variants, and tenascin-C. We identified a specific cell population characterized by the coexpression of nestin, MAP2, and GFAP within the invasion niche of the adamantinomatous subtype. This was especially prominent along the finger-like protrusions. A similar population of presumably astroglial precursors was not visible in other lesions under study, which characterize them as distinct histopathological feature of adaCP. Furthermore, the outer tumor cell layer of adaCP showed a distinct expression of MAP2, a novel finding helpful in the differential diagnosis of epithelial tumors in the sellar region. Our data support the hypothesis that adaCP, unlike other non-neuroepithelial tumors of the central nervous system, create a tumor-specific cellular environment at the tumor-brain junction. Whether this facilitates the characteristic infiltrative growth pattern or is the consequence of an activated Wnt signaling pathway, detectable in 90% of these tumors, will need further consideration.

Gene-environment interactions of selected pharmacogenes in arterial hypertension.

Hypertension affects approximately 1 billion people worldwide. Owing to population aging, hypertension-related cardiovascular burden is expected to rise in the near future. In addition to genetic variants influencing the blood pressure response to antihypertensive drugs, several genes encoding for drug-metabolizing or -transporting enzymes have been associated with blood pressure and/or hypertension in humans (e.g., ACE, CYP1A2, CYP3A5, ABCB1 and MTHFR) regardless of drug treatment. These genes are also involved in the metabolism and transport of endogenous substances and their effects may be modified by selected environmental factors, such as diet or lifestyle. However, little is currently known on the complex interplay between environmental factors, endogenous factors, genetic variants and drugs on blood pressure control. This review will discuss the respective role of population-based primary prevention and personalized medicine for arterial hypertension, taking a pharmacogenomics' perspective focusing on selected pharmacogenes.

Mapping of the genes coding for the two major vaccinia virus core polypeptides.

We have mapped the genes coding for two major structural polypeptides of the vaccinia virus core by hybrid selection and transcriptional mapping. First, RNA was selected by hybridization to restriction fragments of the vaccinia virus genome, translated in vitro and the products were immunoprecipitated with antibodies against the two polypeptides. This approach allowed us to map the genes to the left hand end of the largest Hind III restriction fragment of 50 kilobase pairs. Second, transcriptional mapping of this region of the genome revealed the presence of the two expected RNAs. Both RNAs are transcribed from the leftward reading strand and the 5'-ends of the genes are separated by about 7.5 kilobase pairs of DNA. Thus, two genes encoding structural polypeptides with a similar location in the vaccinia virus particle are clustered at approximately 105 kilobase pairs from the left hand end of the 180 kilobase pair vaccinia virus genome.

Three essays on organizations and their external environment

Abstract: The literature on the various links between organizations and their external environment is very extensive and fragmented. This thesis is comprised of three separate essays, each examining specific research questions related to these links. The first essay deals with the notion of industry life cycle and how the geographical concentration of an industry is linked to the particular life cycle stage in which the industry finds itself. The aim of this first essay is firstly to verify if the evolution of the Swiss hotel industry fits some of the stylized facts of the industry life cycle. The second aim is to verify if there is evidence of geographical clustering of the hotel industry, and by extension of tourism. The third aim is to verify a hypothesis that industry decline manifests itself mainly by company closures in decentralized locations. The importance for organizational survival and performance of adapting and reacting to environmental changes has long been ascertained. This adaptation requires managers, under conditions of uncertainty, to identify relevant changes in their external environment and to interpret the possible effects of those changes on their organization. Furthermore, it requires finding and adopting organizational responses in reaction to the environmental changes. The second essay explores how managers perceive their environment by reporting the results of two workshops held with managers from the European hotel industry. In the third essay we examine in more detail the role of uncertainty in the interpretation by executives of environmental changes. We integrate existing theories of interpretation and uncertainty into one framework, which we then test using national survey data from the hotel industry. In all three essays we are able to provide some evidence to support our main hypotheses, but.also make suggestions far further research into the topics examined.