Molecular evolutionary patterns in the Glomeromycota;

Abstract Arbuscular mycorrhizal fungi (AMF) form symbiosis with roots of approximately 80% of known land plants. These fungi play a key role in the ecology and adaptation of plants to various ecosystems.by increasing the plant resources for various nutrients. Despite their important ecological role, we still have poor understanding of their genetic structure and their molecular evolution. The work presented in this thesis aims to isolate and analyse AMF genes with various molecular techniques, in order to obtain new insights about their genetics, phylogeny and molecular evolution. Some AMF genes were shown through phylogenetic analyses to be more related with plants or mycoparasites than with other fungal organisms. These results led to the prediction that lateral gene transfers (LGT) occurred between AMF and plants during their long-term co-évolution. By phylogenetic and molecular analyses, in the chapter 2 I demonstrate that the hypothesis of LGT is most likely a consequence of analyses carried out on contaminant non AMF-DNA. In addition, various features characteristic of AMF genes have been determined, allowing researchers to scan their own sequence databases for potential non-AMF contaminants. Phylogenetic relationships of AMF with other fungi has been mostly analysed using molecular markers of ribosomal origin. In chapter 2 I successfully isolated gene encoding α- and ß-tubulins from several AMF genera. Consequently, phylogenetic analyses showed that AMF possess an unexpected relationship with ancestral aquatic fungi (chytrids). These results are consistent with the prediction stating that AMF may have played an important role in the colonisation of land by green plants through the establishment of a symbiosis and after the divergence of AMF from aquatic ancestors. In Chapter 4 I tried to isolate the entire AMF gene family encoding P-Type II ATPases, in order to determine their molecular evolution with the fungal kingdom. These genes were further analysed to detect the level of sequence polymorphism that is present within an AMF population. The results obtained show that mutational events previously thought as occurring only among divergent evolutionary lineages (gene duplications, indel mutations in coding regions) can occur within a single population of AMF. These results have far reaching consequences for our understanding of the genetics and ecology of AMF. Résumé Les champignons endomycorrhiziens arbusculaires (CEA) forment une symbiose racinaire avec environ 80% des plantes vasculaires connues. Ces champignons possèdent un rôle important dans l'écologie et l'adaptation des plantes au sein de différents écosystèmes en .augmentant leurs ressources en nutriments. Le travail présenté dans cette thèse se propose d'isoler et d'analyser certains gènes de CEA avec différentes techniques moléculaires à fin d'obtenir de pÌus amples informations concernant l'évolution moléculaire, la phylogénie et leur diversité génétique à diverses échelles taxonomiques. Certaines analyses phylogénétiques des CEA ont conduit à l'hypothèse que des transferts horizontaux de gènes (THG) ont pu avoir lieu durant leur longue co-évolution avec les plantes vasculaires. Dans le chapitre 2 de cette thèse nous démontrons par analyses moléculaire et phylogénétique que l'hypothèse de THG est une conséquence de contaminations à partir d'ADN de plante ou d'autres micro-organismes. De plus, de nombreuses caractéristiques moléculaires de CEA ont pu être déterminées, permettant la mise en place d'un plan à suivre lors de l'analyse de gènes de CEA dans les études futures. Les relations évolutives des. CEA avec d'autres champignons ont été analysées majoritairement à l'aide de marqueurs moléculaires d'origine ribosomiale. Dans les chapitres 2 et 3 j'ai isolé des gènes codant pour l'a- et la ß-tubuline chez différents genres, de CEA. Les analyses phylogénétiques ont démontré une parenté entre les CEA et des champignons aquatiques ancestraux (chytrides). Ces résultats sont en accord avec l'hypothèse selon laquelle les CEA ont probablement joué un rôle primordial dans l'établissement des plantes sur terre à travers une symbiose et suite à leur évolution à partir d'ancêtres vivant dans des milieux aquatiques: Dans le chapitre 4 j'ai isolé une entière famille de gènes chez les CEA codant des ATPases de la membrane plasmique, et étudié leur évolution moléculaire dans le règne des champignons. Ces mêmes gènes ont été analysés ultérieurement à fin de déterminer le degré de polymorphisme de séquence qui peut être présent au sein d'une population de CEA. Les résultats obtenus montrent que des évènements mutationnels considérés comme apparaissant exclusivement dans des lignées évolutives très divergentes (duplication de gènes, insertions/délétions dans des régions transcrites du génome) ont lieu sein d'une même population de CEA. Cette découverte a un impact important sur nos connaissances concernant la génétique des populations des CEA et leur écologie.

Changes in patterns of practice for prostate cancer radiotherapy in Italy 1995-2003. A survey of the Prostate Cancer Study Group of the Italian Radiation Oncology Society.

Aims and background. In 2002, a survey including 1759 patients treated from 1980 to 1998 established a "benchmark" Italian data source for prostate cancer radiotherapy. This report updates the previous one. Methods. Data on clinical management and outcomes of 3001 patients treated in 15 centers from 1999 through 2003 were analyzed and compared with those of the previous survey. Results. Significant differences in clinical management (-10% had abdominal ma-gnetic resonance imaging; +26% received ≥70 Gy, +48% conformal radiotherapy, -20% pelvic radiotherapy) and in G3-4 toxicity rates (-3.8%) were recorded. Actuarial 5-year overall, disease-specific, clinical relapse-free, and biochemical relapse-free survival rates were 88%, 96%, 96% and 88%, respectively. At multivariate analysis, D'Amico risk categories significantly impacted on all the outcomes; higher radiotherapy doses were significantly related with better overall survival rates, and a similar trend was evident for disease-specific and biochemical relapse-free survival; cumulative probability of 5-year late G1-4 toxicity was 24.8% and was significantly related to higher radiotherapy doses (P <0.001). Conclusions. The changing patterns of practice described seem related to an improvement in efficacy and safety of radiotherapy for prostate cancer. However, the impact of the new radiotherapy techniques should be prospectively evaluated.

Swiss behavioural surveillance system 1986-2008

Background: Second generation surveillance is a central feature of HIV/AIDS policy in Switzerland. Behavioural surveys in the general population, men having sex with men (MSM) and injecting drug users (IDU) have been regularly conducted since the early nineties. After peaking at 2144 cases in 1991, the number of new HIV cases notified to the Ministry of Health decreased in each subpopulation until 2000 (n=578) and then rose again to 735 in 2006. The recent increase is mainly due to MSM. Methods: In the general population, representative cross-sectional telephone surveys have been conducted 11 times since 1987. Surveys in convenience samples of MSM, recruited through gay newspapers and gay organisations, have been conducted 5 times since 1992. Surveys among IDU's attending needle exchange programmes have been conducted 5 times since 1993. Condom statistics, available since 1986, are included in the behavioural surveillance system. Results: In the general population aged 17-30, systematic condom use with casual partners in the last six months increased from 8.0% in 1987 to 75.8% in 2007. The proportion of MSM reporting anal intercourse with casual partners in the last 12 months increased from 61% in 1992 to 79% in 2007 (lowest value 56% in 1994) and unprotected anal intercourse with these partners increased from 14 % in 1992 to 24% in 2007 (lowest value 9% in 1994). The proportion of IDUs reporting borrowing used injection equipment decreased from 16.5% in 1993 to 8.9% in 2006. The ratio condoms released to retail/population aged 15-65 increased from 1.68 in 1986 to 3.8 in 2006. Conclusions: It has been possible to maintain a coherent behavioural surveillance system on a long-term basis, allowing for the monitoring of HIV prevention policy outcome and forseeing the development and distribution of new HIV cases in the population.

Low prevalence of behavioural and emotional problems among Swiss paediatric patients with inflammatory bowel disease.

OBJECTIVES: Whether behavioural and emotional maladjustment is more prevalent in children with inflammatory bowel disease (IBD) than in healthy controls remains controversial. The aim of this study was to assess paediatric IBD patients for problems with emotional and behavioural adjustment and to examine associations with clinical and demographic variables. METHODS: Data from paediatric patients with IBD enrolled in the Swiss IBD Cohort Study and the results of both the parent-rated Strengths and Difficulties Questionnaire (SDQ) and the self-reported Child Depression Inventory (CDI) were analysed. Of the 148 registered patients, 126 had at least one questionnaire completed and were included. RESULTS: The mean age of 71 patients with Crohn's disease (44 males, 27 females) was 13.4 years, and 12.8 years for the 55 patients with ulcerative or indeterminate colitis. The mean duration of disease was 1.2 and 2.7 years, respectively. The total score of the SDQ was abnormal in 11.4% of cases compared to 10% in the normal population. Abnormal sub-scores were found in 20.2% of subjects for the domain of emotional problems and in 17.1% for problems with peers. The total CDI T score indicated a significantly lower prevalence of clinical depression in IBD patients than in normal youth. No correlation between the total SDQ scores or the CDI T scores and gender, type or duration of IBD, inflammatory markers or disease scores was found. CONCLUSIONS: The prevalence of problems with behavioural and emotional adjustment among Swiss paediatric IBD patients is low and comparable to that of the normal population.

Beverage preferences and associated drinking patterns, consequences and other substance use behaviours.

BACKGROUND: Studies about beverage preferences in a country in which wine drinking is relatively widespread (like Switzerland) are scarce. Therefore, the main aims of the present study were to examine the associations between beverage preferences and drinking patterns, alcohol-related consequences and the use of other substances among Swiss young men. METHODS: The analytical sample consisted of 5399 Swiss men who participated in the Cohort Study on Substance Use Risk Factors (C-SURF) and had been drinking alcohol over the preceding 12 months. Logistic regression analyses were conducted to study the associations between preference for a particular beverage and (i) drinking patterns, (ii) negative alcohol-related consequences and (iii) the (at-risk) use of cigarettes, cannabis and other illicit drugs. RESULTS: Preference for beer was associated with risky drinking patterns and, comparable with a preference for strong alcohol, with the use of illicit substances (cannabis and other illicit drugs). In contrast, a preference for wine was associated with low-risk alcohol consumption and a reduced likelihood of experiencing at least four negative alcohol-related consequences or of daily cigarette smoking. Furthermore, the likelihood of negative outcomes (alcohol-related consequences; use of other substances) increased among people with risky drinking behaviours, independent of beverage preference. CONCLUSIONS: In our survey, beer preference was associated with risky drinking patterns and illicit drug use. Alcohol polices to prevent large quantities of alcohol consumption, especially of cheaper spirits like beer, should be considered to reduce total alcohol consumption and the negative consequences associated with these beverage types.

Androgen and gonadotropin patterns differ in HIV-1-infected men who develop lipoatrophy during antiretroviral therapy: a case-control study.

OBJECTIVES: We compared androgen and gonadotropin values in HIV-infected men who did and did not develop lipoatrophy on combination antiretroviral therapy (cART). METHODS: From a population of 136 treatment-naïve male Caucasians under successful zidovudine/lamivudine-based cART, the 10 patients developing lipoatrophy (cases) were compared with 87 randomly chosen controls. Plasma levels of free testosterone (fT), dehydroepiandrosterone (DHEA), follicle-stimulating hormone and luteinizing hormone (LH) were measured at baseline and after 2 years of cART. RESULTS: At baseline, 60% of the cases and 71% of the controls showed abnormally low fT values. LH levels were normal or low in 67 and 94% of the patients, respectively, indicating a disturbance of the hypothalamic-pituitary-gonadal axis. fT levels did not significantly change after 2 years of cART. Cases showed a significant increase in LH levels, while controls showed a significant increase in DHEA levels. In a multivariate logistic regression model, lipoatrophy was associated with higher baseline DHEA levels (P=0.04), an increase in LH levels during cART (P=0.001), a lower body mass index and greater age. CONCLUSIONS: Hypogonadism is present in the majority of HIV-infected patients. The development of cART-related lipoatrophy is associated with an increase in LH and a lack of increase in DHEA levels.

Age-associated modulations of cerebral oscillatory patterns related to attention control.

Visual attention depends on bottom-up sensory activation and top-down attentional guidance. Although aging is known to affect sensory processing, its impact on the top-down control of attention remains a matter of debate. We investigated age-related modulations of brain oscillatory activity during visual attention using a variant of the attention network test (ANT) in 20 young and 28 elderly adults. We examined the EEG oscillatory responses to warning and target signals, and explored the correlates of temporal and spatial orienting as well as conflict resolution at target presentation. Time-frequency analysis was performed between 4 and 30Hz, and the relationship between behavioral and brain oscillatory responses was analyzed. Whereas temporal cueing and conflict had similar reaction time effects in both age groups, spatial cueing was more beneficial to older than younger subjects. In the absence of cue, posterior alpha activation was drastically reduced in older adults, pointing to an age-related decline in anticipatory attention. Following both cues and targets, older adults displayed pronounced motor-related activation in the low beta frequency range at the expense of attention-related posterior alpha activation prominent in younger adults. These findings support the recruitment of alternative motor-related circuits in the elderly, in line with the dedifferentiation hypothesis. Furthermore, older adults showed reduced midparietal alpha inhibition induced by temporal orienting as well as decreased posterior alpha activation associated with both spatial orienting and conflict resolution. Altogether, the results are consistent with an overall reduction of task-related alpha activity in the elderly, and provide functional evidence that younger and older adults engage distinct brain circuits at different oscillatory frequencies during attentional functions.

Validation study of the French version of the observer-rater scales measuring coping and cognitive errors (CE-CAP) on a non-clinical population

This study examined the validity and reliability of the French version of two observer-rated measures developed to assess cognitive errors (cognitive errors rating system [CERS]) [6] and coping action patterns (coping action patterns rating system [CAPRS]) [22,24]. The CE measures 14 cognitive errors, broken down according to their valence positive or negative (see the definitions by A.T. Beck), and the CAP measures 12 coping categories, based on an comprehensive review literature, each broken down into three levels of action (affective, behavioural, cognitive). Thirty (N = 30) subjects recruited in a community sample participated in the study. They were interviewed according to a standardized clinical protocol: these interviews were transcribed and analysed with both observer-rated systems. Results showed that the inter-rater reliability of the two measures is good and that their internal validity is satisfactory, due to a non-significant canonical correlation between CAP and CE. With regard to discriminant validity, we found a non-significant canonical correlation between CAPRS and CISS, one of most widely used self-report questionnaire measuring coping. The same can be said for the correlation with a self-report questionnaire measuring symptoms (SCL-90-R). These results confirm the absence of confounds in the assessment of cognitive errors and of coping as assessed by these observer-rated scales and add an argument in favour of the French validation of the CE-CAP rating scales. (C) 2010 Elsevier Masson SAS. All rights reserved.

Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution

Owing to its special mode of evolution and central role in the adaptive immune system, the major histocompatibility complex (MHC) has become the focus of diverse disciplines such as immunology, evolutionary ecology, and molecular evolution. MHC evolution has been studied extensively in diverse vertebrate lineages over the last few decades, and it has been suggested that birds differ from the established mammalian norm. Mammalian MHC genes evolve independently, and duplication history (i.e., orthology) can usually be traced back within lineages. In birds, this has been observed in only 3 pairs of closely related species. Here we report strong evidence for the persistence of orthology of MHC genes throughout an entire avian order. Phylogenetic reconstructions of MHC class II B genes in 14 species of owls trace back orthology over tens of thousands of years in exon 3. Moreover, exon 2 sequences from several species show closer relationships than sequences within species, resembling transspecies evolution typically observed in mammals. Thus, although previous studies suggested that long-term evolutionary dynamics of the avian MHC was characterized by high rates of concerted evolution, resulting in rapid masking of orthology, our results question the generality of this conclusion. The owl MHC thus opens new perspectives for a more comprehensive understanding of avian MHC evolution.

Cardiovascular patterns associated with appetitive and defensive activation during affective picture viewing

Descriptors: cardiovascular patterns, emotion, affective pictures In this study we assessed blood pressure (BP), heart rate (HR), stroke volume (SV), cardiac output (CO), and total peripheral resistance (TPR) in response to 13 picture series in 18 men and 19 women in order to investigate their hemodynamic responses associated with activation of the appetitive and defensive motivational systems underlying emotional experience. Skin conductance level (SCL) was also recorded. BP and SV increased with increasing self-rated arousal both for appetitive and defensive activation, whereas HR decelerated more in response to negative than positive and neutral pictures. TPR showed a general increase from baseline to picture processing but was unrelated to self-rated valence and arousal. These findings suggest that affective modulation of the cardiovascular response to affective pictures is primarily myocardial. The observed response pattern is consistent with a configuration of cardiac sympathetic-parasympathetic coactivation. The relationships between self-reported arousal, BP and SV were mainly exhibited by men suggesting that increases in the sympathetic inotropic effect to the heart with increasing self-rated arousal might be larger in men than in women. In contrast, SCL covaried positively with self-rated arousal both in men and women. This suggests that sex differences in the affective modulation of the responses to pictures may be restricted to specific cardiovascular parameters and support the contention that the sympathetic nervous system does not discharge as a whole.

Temporo-Parietal Junction encodes the Embodied Self: Neuro-Robotics, fMRI, and Lesion mapping.

Introduction: Neuroimaging of the self focused on high-level mechanisms such as language, memory or imagery of the self. Recent evidence suggests that low-level mechanisms of multisensory and sensorimotor integration may play a fundamental role in encoding self-location and the first-person perspective (Blanke and Metzinger, 2009). Neurological patients with out-of body experiences (OBE) suffer from abnormal self-location and the first-person perspective due to a damage in the temporo-parietal junction (Blanke et al., 2004). Although self-location and the first-person perspective can be studied experimentally (Lenggenhager et al., 2009), the neural underpinnings of self-location have yet to be investigated. To investigate the brain network involved in self-location and first-person perspective we used visuo-tactile multisensory conflict, magnetic resonance (MR)-compatible robotics, and fMRI in study 1, and lesion analysis in a sample of 9 patients with OBE due to focal brain damage in study 2. Methods: Twenty-two participants saw a video showing either a person's back or an empty room being stroked (visual stimuli) while the MR-compatible robotic device stroked their back (tactile stimulation). Direction and speed of the seen stroking could either correspond (synchronous) or not (asynchronous) to those of the seen stroking. Each run comprised the four conditions according to a 2x2 factorial design with Object (Body, No-Body) and Synchrony (Synchronous, Asynchronous) as main factors. Self-location was estimated using the mental ball dropping (MBD; Lenggenhager et al., 2009). After the fMRI session participants completed a 6-item adapted from the original questionnaire created by Botvinick and Cohen (1998) and based on questions and data obtained by Lenggenhager et al. (2007, 2009). They were also asked to complete a questionnaire to disclose the perspective they adopted during the illusion. Response times (RTs) for the MBD and fMRI data were analyzed with a 3-way mixed model ANOVA with the in-between factor Perspective (up, down) and the two with-in factors Object (body, no-body) and Stroking (synchronous, asynchronous). Quantitative lesion analysis was performed using MRIcron (Rorden et al., 2007). We compared the distributions of brain lesions confirmed by multimodality imaging (Knowlton, 2004) in patients with OBE with those showing complex visual hallucinations involving people or faces, but without any disturbance of self-location and first person perspective. Nine patients with OBE were investigated. The control group comprised 8 patients. Structural imaging data were available for normalization and co-registration in all the patients. Normalization of each patient's lesion into the common MNI (Montreal Neurological Institute) reference space permitted simple, voxel-wise, algebraic comparisons to be made. Results: Even if in the scanner all participants were lying on their back and were facing upwards, analysis of perspective showed that half of the participants had the impression to be looking down at the virtual human body below them, despite any cues about their body position (Down-group). The other participants had the impression to be looking up at the virtual body above them (Up-group). Analysis of Q3 ("How strong was the feeling that the body you saw was you?") indicated stronger self-identification with the virtual body during the synchronous stroking. RTs in the MBD task confirmed these subjective data (significant 3-way interaction between perspective, object and stroking). fMRI results showed eight cortical regions where the BOLD signal was significantly different during at least one of the conditions resulting from the combination of Object and Stroking, relative to baseline: right and left temporo-parietal junction, right EBA, left middle occipito-temporal gyrus, left postcentral gyrus, right medial parietal lobe, bilateral medial occipital lobe (Fig 1). The activation patterns in right and left temporo-parietal junction and right EBA reflected changes in self-location and perspective as revealed by statistical analysis that was performed on the percentage of BOLD change with respect to the baseline. Statistical lesion overlap comparison (using nonparametric voxel based lesion symptom mapping) with respect to the control group revealed the right temporo-parietal junction, centered at the angular gyrus (Talairach coordinates x = 54, y =-52, z = 26; p>0.05, FDR corrected). Conclusions: The present questionnaire and behavioural results show that - despite the noisy and constraining MR environment) our participants had predictable changes in self-location, self-identification, and first-person perspective when robotic tactile stroking was applied synchronously with the robotic visual stroking. fMRI data in healthy participants and lesion data in patients with abnormal self-location and first-person perspective jointly revealed that the temporo-parietal cortex especially in the right hemisphere encodes these conscious experiences. We argue that temporo-parietal activity reflects the experience of the conscious "I" as embodied and localized within bodily space.

Existential behavioural therapy for informal caregivers of palliative patients: a randomised controlled trial.

BACKGROUND: Existential behavioural therapy (EBT) was developed to support informal caregivers of palliative patients in the last stage of life and during bereavement as a manualised group psychotherapy comprising six sessions. We tested the effectiveness of EBT on mental stress and quality of life (QOL). METHODS: Informal caregivers were randomly assigned (1:1) to EBT or a treatment-as-usual control group using computer-generated numbers in blocks of 10. Primary outcomes were assessed with the Brief Symptom Inventory (subscales somatisation, anxiety and depression), the Satisfaction with Life Scale (SWLS), the WHOQOL-BREF and a numeric rating scale for QOL (QOL-NRS, range 0-10). Data were collected at baseline, pre-treatment, post-treatment and follow-ups after 3 and 12âeuro0/00months. Treatment effects were assessed with a multivariate analysis of covariance. RESULTS: Out of 160 relatives, 81 were assigned to EBT and 79 to the control group. Participants were 54.5âeuro0/00±âeuro0/0013.2âeuro0/00years old; 69.9% were female. The multivariate model was significant for the pre-/post-comparison (pâeuro0/00=âeuro0/000.005) and the pre-/12-month comparison (pâeuro0/00=âeuro0/000.05) but not for the pre-/3-month comparison. Medium to large effects on anxiety and QOL (SWLS, WHOQOL-BREF, QOL-NRS) were found at post-treatment; medium effects on depression and QOL (QOL-NRS) emerged in the 12-month follow-up. No adverse effects of the intervention were observed. CONCLUSION: Existential behavioural therapy appears to exert beneficial effects on distress and QOL of informal caregivers of palliative patients. Further longitudinal evidence is needed to confirm these findings. Copyright © 2013 John Wiley & Sons, Ltd.

Consultation d'urgence/crise pour couples et families: motifs d'urgence et évaluation du traitement [Couples and families emergency/crisis consultation: emergency patterns and treatment assessment]

Since the opening in 2003 of the Couple & Family Consultation Unit (UCCF) at Prangins Hospital, we have met urgent demands and observed that the suffering systems (i.e., couples and families) couldn't face any waiting period. So in 2007 an Emergency/Crisis Facility was created, based on the hypothesis that there is no contra-indication to systemic emergency care, if one understands and structures both crisis and treatment. We studied the suffering population in demand and the emergency/crisis issues and assessed therapy efficiency. Then we observed that treating suffering systems in emergency does produce therapeutic gain in terms of crisis resolution and patients' satisfaction. Those treatments refer to public health issues, as considered the human, social and financial cost of couples/families dysfunctions.

Climatic extremes improve predictions of spatial patterns of tree species.

Understanding niche evolution, dynamics, and the response of species to climate change requires knowledge of the determinants of the environmental niche and species range limits. Mean values of climatic variables are often used in such analyses. In contrast, the increasing frequency of climate extremes suggests the importance of understanding their additional influence on range limits. Here, we assess how measures representing climate extremes (i.e., interannual variability in climate parameters) explain and predict spatial patterns of 11 tree species in Switzerland. We find clear, although comparably small, improvement (+20% in adjusted D(2), +8% and +3% in cross-validated True Skill Statistic and area under the receiver operating characteristics curve values) in models that use measures of extremes in addition to means. The primary effect of including information on climate extremes is a correction of local overprediction and underprediction. Our results demonstrate that measures of climate extremes are important for understanding the climatic limits of tree species and assessing species niche characteristics. The inclusion of climate variability likely will improve models of species range limits under future conditions, where changes in mean climate and increased variability are expected.