Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals?

Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.

Patterns of molecular evolution in dioecious and non-dioecious Silene.

Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from a high probability of extinction in dioecious species because of less efficient dispersal and the costs of sexual selection, which are expected to harm dioecious species' survival on the long term. These handicaps should decrease the effective population size (Ne) of dioecious species, which in turn should reduce the efficacy of selection. Moreover, sexual selection in dioecious species is expected to specifically affect some genes, which will evolve under positive selection. The relative contribution of these effects is currently unknown and we tried to disentangle them by comparing sequence evolution between dioecious and non-dioecious species in the Silene genus (Caryophyllaceae), where dioecy has evolved at least twice. For the dioecious species in the section Melandrium, where dioecy is the oldest, we found a global reduction of purifying selection, while on some, male-biased genes, positive selection was found. For section Otites, where dioecy evolved more recently, we found no significant differences between dioecious and non-dioecious species. Our results are consistent with the view that dioecy is an evolutionary dead end in flowering plants, although other scenarios for explaining reduced Ne cannot be ruled out. Our results also show that contrasting forces act on the genomes of dioecious plants, and suggest that some time is required before the genome of such plants bears the footprints of dioecy.

[Verbal and nonverbal dichotic listening test. Influence of the hemispheric activation state in normal subjects]. / Test D'écoute dichotique verbal et non verbal. Influence de l'état d'activation hémisphérique chez le sujet normal.

The dichotomic listening test provides data for assessment of cerebral hemisphere activities in response to a given stimulus. Variations in results following verbal and non-verbal dichotomic listening tests to familiar sounds are described, as well as modifications when the activity of one or other hemisphere has been previously altered. Findings demonstrate that voluntary excentration of gaze modifies inter-hemispheric equilibrium and affects the results of the non-verbal dichotomic listening test.

[Prospective study of favorable factors in follow-up of drug addicted patients--apropos of 257 patients of the Cassini Center in Paris]. / Recherche prospective de facteurs favorisant le suivi des toxicomanes--à propos de 257 patients du centre Cassini de Paris.

UNLABELLED: Assessing the effectiveness of treatment is one of the main concerns of any medical process. The different ways proposed for assuming the responsibility of drug addicts and their efficacy are greatly heterogeneous since drug-abusing takes on diverse forms. Thus, in order to closely target the request of drug addicts and adjust their follow-up, we undertook to study prospectively, for 3 months, a population of drug addicts taking medical advice for the first time at the Cassini center in Paris, with the assumption that some predictors may forecast outcomes. METHOD: Data were obtained at the admission with a structured interview about socio-economic and demographic status, psychiatric disorders (assessed clinically according to DSM III-R and with HAD and MADRS scales), substance use and prior treatment history, environmental data (as well as familial substance use or support lending). Medical and paramedical referents have been interviewed after their first contact with the patient about his expectations and his motivation. Familial attendance at this first contact was noted as well as its implication in the programme. At the end of the study, we noted length of stay, regularity of follow up and clinical changes with a last interview of the staff. RESULTS: Half the time, patients' follow up doesn't last a month, drug abuse doesn't change in 6 out of 10 cases, and we only note 14% of durable abstinence. Polydrug abuse (over 80%) is not linked, here, with pejorative outcomes, in opposition to the usual literature. Heroin is the main substance used by our population (over 80%), other opiates, sedatives and alcohol are associated by more than 30% of these patients; cocaine is associated in a quarter of the cases. More than 10% of the patients are concerned by ecstasy and LSD. Cannabis use is common. Medical complaint (mainly viral diseases) at the beginning of the programme, concerns one of two patients. Only a few are initially known as being HIV positive, suggesting a great lack of information. Over forty percent of the patients are given a DSM III-R diagnosis at the end of the first medical advice, when a doubt subsists for a third of the other patients. Major depressive disorder for the first axis and borderline personality disorder for the second axis are the main disorders we founded. We also noted a large ratio (n = 13.5%) of schizophrenic disorders. Univariate analysis: length and regularity of the programmes are key factors of their efficacy. A long follow-up is also required to improve patients' socio-economical status. Initial psychiatric disorders are linked, in our study as well as in literature, with longer stays in therapeutic programms. By revenge, psychiatric disorders at the third month (over 10%) are linked with poorer outcomes. We noted with interest that, in our sample, neither imprisonment in the past (over 40%, but we noted several imprisonments in a case out of two), or intraveinous route at any moment of the patient's life time (40%), or else a programm caused by a court (a quarter of the patients) are of wrong prognosis. Relatives' implication in the programm is linked with favorable outcomes. Multivariate analysis draws 3 independent clusters about the length of stay. One concerns patient's motivation as assessed by medical staff. An other one concerns patient's relatives' implication in the care. A third one is about the begining of the treatment: an initial medical prescrition and a psychological help are linked with favorable outcomes. About the efficacy, multivariate analysis isolates 4 independant clusters. Prior drug abuse programmes (one out of three patients) are associated with poorer outcomes, when, by revenge, familial relationship initially seen by the patient as (very) satisfying, patient's motivation, and, again, an initial medical prescription are linked with better outcomes. The study of those of the patients whose programme lasted more then 3 months but without any appreciable benefit shows that a long follow-up is successful when it is regular, when it provides a socio-economical status improvement and when the patient is given access to insight. For these patients, the (old) age is associated with better outcomes. By revenge, such a 3 months follow-up is not able to reduce drug abuse when a psychiatric disorder exists at the third month. Patients whose treatment was referred by a court don't differ from the others: their length of stay and outcomes are the same. DISCUSSION: Our study confirms our initial hypothesis according to witch subgroups in our population of drug abusers should be isolated and that some predictors of outcomes should be described. Three points seem important to be discussed. First, a medical prescription appears to be important to initiate the relationship between the patient and his practicioner. We have never see any report about this particular point. (ABSTRACT TRUNCATED)

[Depression and somatic diseases. On one retrospective study of 210 patients with major depression hospitalized in a psychiatric hospital]. / Dépression et maladies somatiques. A propos d'une étude rétrospective de 210 épisodes dépressifs majeurs hospitalisés en psychiatrie.

Associations between depression and somatic disorders are common and little studied. We present the results of a retrospective study including 210 psychiatric inpatients, suffering from a major depressive episodes (MDE-DSM III-R criteria). The purpose of this study was: first, to access the prevalence of comorbid MDEs with somatic illness, second to describe the clinical, therapeutic and evolutionary characteristics of MDEs secondary to a physical trouble, comparatively with primary depressions and depressions secondary to another psychiatric disorder. A somatic comorbidity was found in 55% of patients (n = 116), the physical illness being, in 6% of cases, causal regarding MDEs. MDEs with a somatic comorbidity (n = 55) are significantly different from primary MDEs (n = 36) and MDEs secondary to another psychiatric disorder (n = 58), regarding an older age at hospitalization and at first affective episode. Moreover, they are different from MDEs secondary to another psychiatric disorder through fewer past suicide attempts, more episodes with melancholic or psychotic characteristics and a lower frequency of tricyclic antidepressant use. Despite methodologically limited, these results confirm the frequency of physical comorbidity in depressed patients hospitalized in general hospitals, especially in elderly subjects. They also reflect the heterogeneity of the group of secondary depressions, MDEs associated with a somatic illness being closer to MDEs secondary to another psychiatric disorder than to primary MDEs.

[Drug dependence and psychotropic drugs]. / Pharmaco-dépendance et psychotropes.

Although the utility of psychotropic drugs has been well demonstrated, caution must still be exercised in their use. Among their potential risks, drug dependency must be kept in mind. This risk is well accepted with regard to benzodiazepines, and it appeared useful to study the potential risk for antidepressants, neuroleptics and thymoregulatory agents. Whatever the drug, the predominant factor appears to be psychological dependency. Prevention of drug dependency is most often achieved by informing the patient, limiting the length of use of the drug, making regular reevaluation of symptoms and of drug indication, and frequently be establishing a "treatment contract". The importance of the patient-physician relationship in the prescription of such treatment must be underlined.