Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.

Experimental support for the make-up hypothesis in nestling tawny owls (Strix aluco)

Body condition can affect coloration of traits used in sexual selection and parent-offspring communication by inducing rapid internal changes in pigment concentration or aggregation, thickness of collagen arrays, or blood flux. The recent "makeup hypothesis" proposes an alternative honesty-reinforcing mechanism, with behaviorally mediated deposition of substances on body surfaces ("cosmetics") generating covariation between body condition and coloration. In birds, the uropygial gland wax is actively spread on feathers using the bill and changes in its deposition rate may cause rapid changes in bill and plumage coloration. Using tawny owl nestlings, we tested 3 predictions of the makeup hypothesis, namely that 1) quantity of preen wax deposited accounts for variation in bill coloration, 2) an immune stimulation (induced by injection of a lipopolysaccharide [LPS]) impairs uropygial gland wax production, and 3) different intensities of immune stimulations (strong vs. weak stimulations induced by injections of either LPS or phytohemagglutinin [PHA], respectively) and high versus low food availabilities result in different bill colorations. We found that 1) preen wax reduced bill brightness, 2) a challenge with LPS impaired uropygial gland development, and 3) nestlings challenged with LPS had a brighter bill than PHA-injected nestlings, whereas diet manipulation had no significant effect. Altogether, these results suggest that a strong immune challenge may decrease preen wax deposition rate on the bill of nestling birds, at least by impairing gland wax production, which causes a change in bill coloration. Our study therefore highlights that cosmetic colors might signal short-term variation in immunological status.

Functional analysis of human POT1 and RPA : insights into the role of single stranded DNA binding proteins at telomeres

Abstract Telomeres, the natural ends of chromosomes, need to be protected from chromosome end fusions, aberrant homologous recombination and degradation. In humans, chromosome ends are specified through arrays of tandemly repeated 5'-TTAGGG-3' hexamers, ending in a 3' overhang. A complex formed by the six proteins TRF1, TRF2, hRap1, TIN2, TPP1 and POT1 specifically assocìates with and protects telomeres. Telomeres are maintained by semiconservative DNA replication and by a specialized reverse transcriptase, telomerase, that carries an RNA subunit which templates new telomeric repeat synthesis. The telomeric single stranded (ss) DNA binding protein POT1 protects the telomeric 3' overhang and modulates telomerase-mediated telomere elongation. It is possible that POT1 also influences DNA synthesis during semiconservative DNA replication, which is initiated by the DNA polymerase alpha-primase complex. The heterotrimeric ss DNA-binding protein RPA plays essential roles during DNA replication. RPA binds to ss DNA with high affinity in order to stabilize ss DNA and facilitate nascent strand synthesis at the replication fork. Here we investigate how the two proteins RPA and POT1 contribute to telomere maintenance by regulating semi-conservative DNA replication and telomerase. Using chromatin immunoprecipitation experiments, we show that RPA associates with telomeres during S-phase. Analysis of telomere structure in cells shRNA-depleted for RPA and POT1 reveals that loss of RPA and POT1 causes exposure of single-stranded DNA at telomeres, suggestive of incomplete DNA replication. Biochemical experiments using purified recombinant POT1 and RPA show that saturating telomeric oligonucleotides with POT1 or RPA reduces the primase activity of the DNA polymerase alpha-primase complex and the overall activity of telomerase. POT1 and RPA also increase the primer extension by DNA polymerase alpha-primase complex and the processivity of telomerase under certain conditions, although POT1 increases the activities to a greater extent than RPA. We propose that POT1 is required for proper replication of the lagging strand of telomeres and that some phenotypes observed in POT1-depleted cells may stern from incomplete DNA replication rather than de-protection of the single-stranded overhang. Résumé Les télomères, les extrémités normales des chromosomes linéaires, doivent être protégés des fusions chromosomiques, d'événements de recombinaison homologue aberrants et de phénomènes de dégradation. Chez l'Homme, les extrémités des chromosomes sont constitués d'ADN double brin répétitif de séquence 5'-TTAGGG-3', d'une extension simple brin 3' sortante et d'un complexe protéique formé des six facteurs TRF1, TRF2, hRap1, TIN2, TPP1 et POT1 qui, s'associant à cette séquence, protègent l'ADN télomèrique. Les télomères sont maintenus par la télomérase, une transcriptase inverse capable d'allonger l'extension 3' sortante télomérique. POT1 lie l'ADN simple brin télomérique et module l'élongation des télomères par la télomérase. POT1 pourrait en théorie également influencer la réplication semi-conservative de l'ADN. L'ADN-polymérase Pal alpha-primase amorce et initie la synthèse d'ADN. Pendant la réplication, l'ADN simple brin est stabilisé par RPA, un complexe hétérotrimèrique qui lie l'ADN simple brin. RPA facilite la synthèse du brin naissant à la fourche de réplication. Ici nous avons étudié comment ces deux protéines qui lient l'ADN simple brin, RPA et POT1, régulent la réplication des télomères par la télomérase et la machinerie classique de réplication de l'ADN. Par immunoprécipitation de chromatine (ChIP), nous montrons que RPA est localisé aux télomères lors de la phase S du cycle cellulaire. De plus, l'analyse de la structure des télomeres indique que !a perte de RPA ou de POT1 conduit à l'apparition d'ADN simple brin télomérique, suggérant une réplication incomplète de l'ADN télomérique in vivo. Par une approche complémentaire biochimique utilisant les protéines POT1 et RPA recombinantes purifiées, nous montrons également que la liaison de POT1 ou de RPA à des oligonucléotides télomériques bloque l'activité primase du complexe polymérase alpha/primase et réduit l'activité télomérase sur ces substrats. En revanche, leur liaison augmente l'activité ADN-polymérase du complexe polymérase alpha/primase, ainsi que fa processivité de la télomérase dans certaines conditions, POT1 étant le plus efficace des deux facteurs. Nous proposons que POT1 est nécessaire à la réplication du brin retardé au niveau des télomères, ce qui suggère que certains phénotypes des cellules déplétés en POT1 puissent résulter d'une réplication incomplète de l'ADN télémétrique plutôt que d'une déprotection de l'extrémité sortante des télomères.

Exact representation of antenna system diversity performance from input parameter description

A simplc formulation Io compute thc envelope correlation of anantenna divemiry system is dcrired. 11 is shown how to compute theenvelope correlation hom the S-parameter descnplian of the antennasystem. This approach has the advantage that i t does not require thecomputation nor the measurement of the radiation panem of theantenna system. It also offers the advantage of providing a clcaunderstanding ofthe effects ofmutual coupling and input match on thediversity performance of the antcnnii system.

Changing landscapes of Switzerland: assessing effects of historic and future land uses and land covers on the occurrence of selected butterfly species

Summary Landscapes are continuously changing. Natural forces of change such as heavy rainfall and fires can exert lasting influences on their physical form. However, changes related to human activities have often shaped landscapes more distinctly. In Western Europe, especially modern agricultural practices and the expanse of overbuilt land have left their marks in the landscapes since the middle of the 20th century. In the recent years men realised that mare and more changes that were formerly attributed to natural forces might indirectly be the result of their own action. Perhaps the most striking landscape change indirectly driven by human activity we can witness in these days is the large withdrawal of Alpine glaciers. Together with the landscapes also habitats of animal and plant species have undergone vast and sometimes rapid changes that have been hold responsible for the ongoing loss of biodiversity. Thereby, still little knowledge is available about probable effects of the rate of landscape change on species persistence and disappearance. Therefore, the development and speed of land use/land cover in the Swiss communes between the 1950s and 1990s were reconstructed using 10 parameters from agriculture and housing censuses, and were further correlated with changes in butterfly species occurrences. Cluster analyses were used to detect spatial patterns of change on broad spatial scales. Thereby, clusters of communes showing similar changes or transformation rates were identified for single decades and put into a temporally dynamic sequence. The obtained picture on the changes showed a prevalent replacement of non-intensive agriculture by intensive practices, a strong spreading of urban communes around city centres, and transitions towards larger farm sizes in the mountainous areas. Increasing transformation rates toward more intensive agricultural managements were especially found until the 1970s, whereas afterwards the trends were commonly negative. However, transformation rates representing the development of residential buildings showed positive courses at any time. The analyses concerning the butterfly species showed that grassland species reacted sensitively to the density of livestock in the communes. This might indicate the augmented use of dry grasslands as cattle pastures that show altered plant species compositions. Furthermore, these species also decreased in communes where farms with an agricultural area >5ha have disappeared. The species of the wetland habitats were favoured in communes with smaller fractions of agricultural areas and lower densities of large farms (>10ha) but did not show any correlation to transformation rates. It was concluded from these analyses that transformation rates might influence species disappearance to a certain extent but that states of the environmental predictors might generally outweigh the importance of the corresponding rates. Information on the current distribution of species is evident for nature conservation. Planning authorities that define priority areas for species protection or examine and authorise construction projects need to know about the spatial distribution of species. Hence, models that simulate the potential spatial distribution of species have become important decision tools. The underlying statistical analyses such as the widely used generalised linear models (GLM) often rely on binary species presence-absence data. However, often only species presence data have been colleted, especially for vagrant, rare or cryptic species such as butterflies or reptiles. Modellers have thus introduced randomly selected absence data to design distribution models. Yet, selecting false absence data might bias the model results. Therefore, we investigated several strategies to select more reliable absence data to model the distribution of butterfly species based on historical distribution data. The results showed that better models were obtained when historical data from longer time periods were considered. Furthermore, model performance was additionally increased when long-term data of species that show similar habitat requirements as the modelled species were used. This successful methodological approach was further applied to assess consequences of future landscape changes on the occurrence of butterfly species inhabiting dry grasslands or wetlands. These habitat types have been subjected to strong deterioration in the recent decades, what makes their protection a future mission. Four spatially explicit scenarios that described (i) ongoing land use changes as observed between 1985 and 1997, (ii) liberalised agricultural markets, and (iii) slightly and (iv) strongly lowered agricultural production provided probable directions of landscape change. Current species-environment relationships were derived from a statistical model and used to predict future occurrence probabilities in six major biogeographical regions in Switzerland, comprising the Jura Mountains, the Plateau, the Northern and Southern Alps, as well as the Western and Eastern Central Alps. The main results were that dry grasslands species profited from lowered agricultural production, whereas overgrowth of open areas in the liberalisation scenario might impair species occurrence. The wetland species mostly responded with decreases in their occurrence probabilities in the scenarios, due to a loss of their preferred habitat. Further analyses about factors currently influencing species occurrences confirmed anthropogenic causes such as urbanisation, abandonment of open land, and agricultural intensification. Hence, landscape planning should pay more attention to these forces in areas currently inhabited by these butterfly species to enable sustainable species persistence. In this thesis historical data were intensively used to reconstruct past developments and to make them useful for current investigations. Yet, the availability of historical data and the analyses on broader spatial scales has often limited the explanatory power of the conducted analyses. Meaningful descriptors of former habitat characteristics and abundant species distribution data are generally sparse, especially for fine scale analyses. However, this situation can be ameliorated by broadening the extent of the study site and the used grain size, as was done in this thesis by considering the whole of Switzerland with its communes. Nevertheless, current monitoring projects and data recording techniques are promising data sources that might allow more detailed analyses about effects of long-term species reactions on landscape changes in the near future. This work, however, also showed the value of historical species distribution data as for example their potential to locate still unknown species occurrences. The results might therefore contribute to further research activities that investigate current and future species distributions considering the immense richness of historical distribution data. Résumé Les paysages changent continuellement. Des farces naturelles comme des pluies violentes ou des feux peuvent avoir une influence durable sur la forme du paysage. Cependant, les changements attribués aux activités humaines ont souvent modelé les paysages plus profondément. Depuis les années 1950 surtout, les pratiques agricoles modernes ou l'expansion des surfaces d'habitat et d'infrastructure ont caractérisé le développement du paysage en Europe de l'Ouest. Ces dernières années, l'homme a commencé à réaliser que beaucoup de changements «naturels » pourraient indirectement résulter de ses propres activités. Le changement de paysage le plus apparent dont nous sommes témoins de nos jours est probablement l'immense retraite des glaciers alpins. Avec les paysages, les habitats des animaux et des plantes ont aussi été exposés à des changements vastes et quelquefois rapides, tenus pour coresponsable de la continuelle diminution de la biodiversité. Cependant, nous savons peu des effets probables de la rapidité des changements du paysage sur la persistance et la disparition des espèces. Le développement et la rapidité du changement de l'utilisation et de la couverture du sol dans les communes suisses entre les années 50 et 90 ont donc été reconstruits au moyen de 10 variables issues des recensements agricoles et résidentiels et ont été corrélés avec des changements de présence des papillons diurnes. Des analyses de groupes (Cluster analyses) ont été utilisées pour détecter des arrangements spatiaux de changements à l'échelle de la Suisse. Des communes avec des changements ou rapidités comparables ont été délimitées pour des décennies séparées et ont été placées en séquence temporelle, en rendrent une certaine dynamique du changement. Les résultats ont montré un remplacement répandu d'une agriculture extensive des pratiques intensives, une forte expansion des faubourgs urbains autour des grandes cités et des transitions vers de plus grandes surfaces d'exploitation dans les Alpes. Dans le cas des exploitations agricoles, des taux de changement croissants ont été observés jusqu'aux années 70, alors que la tendance a généralement été inversée dans les années suivantes. Par contre, la vitesse de construction des nouvelles maisons a montré des courbes positives pendant les 50 années. Les analyses sur la réaction des papillons diurnes ont montré que les espèces des prairies sèches supportaient une grande densité de bétail. Il est possible que dans ces communes beaucoup des prairies sèches aient été fertilisées et utilisées comme pâturages, qui ont une autre composition floristique. De plus, les espèces ont diminué dans les communes caractérisées par une rapide perte des fermes avec une surface cultivable supérieure à 5 ha. Les espèces des marais ont été favorisées dans des communes avec peu de surface cultivable et peu de grandes fermes, mais n'ont pas réagi aux taux de changement. Il en a donc été conclu que la rapidité des changements pourrait expliquer les disparitions d'espèces dans certains cas, mais que les variables prédictives qui expriment des états pourraient être des descripteurs plus importants. Des informations sur la distribution récente des espèces sont importantes par rapport aux mesures pour la conservation de la nature. Pour des autorités occupées à définir des zones de protection prioritaires ou à autoriser des projets de construction, ces informations sont indispensables. Les modèles de distribution spatiale d'espèces sont donc devenus des moyens de décision importants. Les méthodes statistiques courantes comme les modèles linéaires généralisés (GLM) demandent des données de présence et d'absence des espèces. Cependant, souvent seules les données de présence sont disponibles, surtout pour les animaux migrants, rares ou cryptiques comme des papillons ou des reptiles. C'est pourquoi certains modélisateurs ont choisi des absences au hasard, avec le risque d'influencer le résultat en choisissant des fausses absences. Nous avons établi plusieurs stratégies, basées sur des données de distribution historique des papillons diurnes, pour sélectionner des absences plus fiables. Les résultats ont démontré que de meilleurs modèles pouvaient être obtenus lorsque les données proviennent des périodes de temps plus longues. En plus, la performance des modèles a pu être augmentée en considérant des données de distribution à long terme d'espèces qui occupent des habitats similaires à ceux de l'espèce cible. Vu le succès de cette stratégie, elle a été utilisée pour évaluer les effets potentiels des changements de paysage futurs sur la distribution des papillons des prairies sèches et marais, deux habitats qui ont souffert de graves détériorations. Quatre scénarios spatialement explicites, décrivant (i) l'extrapolation des changements de l'utilisation de sol tels qu'observés entre 1985 et 1997, (ii) la libéralisation des marchés agricoles, et une production agricole (iii) légèrement amoindrie et (iv) fortement diminuée, ont été utilisés pour générer des directions de changement probables. Les relations actuelles entre la distribution des espèces et l'environnement ont été déterminées par le biais des modèles statistiques et ont été utilisées pour calculer des probabilités de présence selon les scénarios dans six régions biogéographiques majeures de la Suisse, comportant le Jura, le Plateau, les Alpes du Nord, du Sud, centrales orientales et centrales occidentales. Les résultats principaux ont montré que les espèces des prairies sèches pourraient profiter d'une diminution de la production agricole, mais qu'elles pourraient aussi disparaître à cause de l'embroussaillement des terres ouvertes dû à la libéralisation des marchés agricoles. La probabilité de présence des espèces de marais a décrû à cause d'une perte générale des habitats favorables. De plus, les analyses ont confirmé que des causes humaines comme l'urbanisation, l'abandon des terres ouvertes et l'intensification de l'agriculture affectent actuellement ces espèces. Ainsi ces forces devraient être mieux prises en compte lors de planifications paysagères, pour que ces papillons diurnes puissent survivre dans leurs habitats actuels. Dans ce travail de thèse, des données historiques ont été intensivement utilisées pour reconstruire des développements anciens et pour les rendre utiles à des recherches contemporaines. Cependant, la disponibilité des données historiques et les analyses à grande échelle ont souvent limité le pouvoir explicatif des analyses. Des descripteurs pertinents pour caractériser les habitats anciens et des données suffisantes sur la distribution des espèces sont généralement rares, spécialement pour des analyses à des échelles fores. Cette situation peut être améliorée en augmentant l'étendue du site d'étude et la résolution, comme il a été fait dans cette thèse en considérant toute la Suisse avec ses communes. Cependant, les récents projets de surveillance et les techniques de collecte de données sont des sources prometteuses, qui pourraient permettre des analyses plus détaillés sur les réactions à long terme des espèces aux changements de paysage dans le futur. Ce travail a aussi montré la valeur des anciennes données de distribution, par exemple leur potentiel pour aider à localiser des' présences d'espèces encore inconnues. Les résultats peuvent contribuer à des activités de recherche à venir, qui étudieraient les distributions récentes ou futures d'espèces en considérant l'immense richesse des données de distribution historiques.

The yield of high-density electric source imaging in focal epilepsy

Background: EEG is the cornerstone of epilepsy diagnostics and mandatory to determine the underlying epilepsy syndrome (e.g. focal vs idiopathic generalized). However, its potential as imaging tool is still underrecognized. In the present study, we aim to determine the prerequisites of maximal benefit of electric source imaging (ESI) to localize the irritative zone in patients with focal epilepsy. Methods: 150 patients suffering from focal epilepsy and with minimum 1 year post-operative follow-up were studied prospectively by reviewers blinded to the underlying diagnosis and outcome. We evaluated the influence of two important factors on sensitivity and specificity of ESI: the number of electrodes (low resolution, LR-ESI: \30 vs. high resolution, HR-ESI: 128-256 electrodes), and the use of individual MRI (i-MRI) vs. template MRI (t-MRI) as head model.Results: ESI had a sensitivity of 85% and a specificity of 87% when HR-ESI with i-MRI was used. Using LR-ESI, sensitivity decreased to 68%, or even 57% when only t-MRI was available. The sensitivity of HR-ESI/i-MRI compared favorably with those of MRI (76%), PET (69%) and ictal/interictal SPECT (64%).Interpretation: This study on a large patient group shows excellent sensitivity and specificity of ESI if 128 EEG channels or more are used for ESI and if the results are co-registered to the patient's individual MRI. Localization precision is as high as or even higher than established brain imaging techniques, providing excellent costeffectiveness in epilepsy evaluation. HR-ESI appears to be a valuable additional imaging tool, given that larger electrode arrays are easily and rapidly applied with modern EEG equipment and that structural MRI is nearly always available for these patients.

Nets: Network estimation for time series

This work proposes novel network analysis techniques for multivariate time series.We define the network of a multivariate time series as a graph where verticesdenote the components of the process and edges denote non zero long run partialcorrelations. We then introduce a two step LASSO procedure, called NETS, toestimate high dimensional sparse Long Run Partial Correlation networks. This approachis based on a VAR approximation of the process and allows to decomposethe long run linkages into the contribution of the dynamic and contemporaneousdependence relations of the system. The large sample properties of the estimatorare analysed and we establish conditions for consistent selection and estimation ofthe non zero long run partial correlations. The methodology is illustrated with anapplication to a panel of U.S. bluechips.

Integrated Analysis of High-Resolution Gene Expression and Copy Number Profiling Identified Biallelic Deletion of CDKN2A/2B Tumor Suppressor Locus As the Most Frequent and Unique Genomic Abnormality in Diffuse Large B-Cell Lymphoma (DLBCL) with Strong Prognostic Value in Both GCB and ABC Subtypes and Not Overcome by a Dose-Intensive Immunochemotherapy Regimen Plus Rituximab. Results of a Prospective GELA Clinical Trial Program

Background and aim of the study: Genomic gains and losses play a crucial role in the development and progression of DLBCL and are closely related to gene expression profiles (GEP), including the germinal center B-cell like (GCB) and activated B-cell like (ABC) cell of origin (COO) molecular signatures. To identify new oncogenes or tumor suppressor genes (TSG) involved in DLBCL pathogenesis and to determine their prognostic values, an integrated analysis of high-resolution gene expression and copy number profiling was performed. Patients and methods: Two hundred and eight adult patients with de novo CD20+ DLBCL enrolled in the prospective multicentric randomized LNH-03 GELA trials (LNH03-1B, -2B, -3B, 39B, -5B, -6B, -7B) with available frozen tumour samples, centralized reviewing and adequate DNA/RNA quality were selected. 116 patients were treated by Rituximab(R)-CHOP/R-miniCHOP and 92 patients were treated by the high dose (R)-ACVBP regimen dedicated to patients younger than 60 years (y) in frontline. Tumour samples were simultaneously analysed by high resolution comparative genomic hybridization (CGH, Agilent, 144K) and gene expression arrays (Affymetrix, U133+2). Minimal common regions (MCR), as defined by segments that affect the same chromosomal region in different cases, were delineated. Gene expression and MCR data sets were merged using Gene expression and dosage integrator algorithm (GEDI, Lenz et al. PNAS 2008) to identify new potential driver genes. Results: A total of 1363 recurrent (defined by a penetrance > 5%) MCRs within the DLBCL data set, ranging in size from 386 bp, affecting a single gene, to more than 24 Mb were identified by CGH. Of these MCRs, 756 (55%) showed a significant association with gene expression: 396 (59%) gains, 354 (52%) single-copy deletions, and 6 (67%) homozygous deletions. By this integrated approach, in addition to previously reported genes (CDKN2A/2B, PTEN, DLEU2, TNFAIP3, B2M, CD58, TNFRSF14, FOXP1, REL...), several genes targeted by gene copy abnormalities with a dosage effect and potential physiopathological impact were identified, including genes with TSG activity involved in cell cycle (HACE1, CDKN2C) immune response (CD68, CD177, CD70, TNFSF9, IRAK2), DNA integrity (XRCC2, BRCA1, NCOR1, NF1, FHIT) or oncogenic functions (CD79b, PTPRT, MALT1, AUTS2, MCL1, PTTG1...) with distinct distribution according to COO signature. The CDKN2A/2B tumor suppressor locus (9p21) was deleted homozygously in 27% of cases and hemizygously in 9% of cases. Biallelic loss was observed in 49% of ABC DLBCL and in 10% of GCB DLBCL. This deletion was strongly correlated to age and associated to a limited number of additional genetic abnormalities including trisomy 3, 18 and short gains/losses of Chr. 1, 2, 19 regions (FDR < 0.01), allowing to identify genes that may have synergistic effects with CDKN2A/2B inactivation. With a median follow-up of 42.9 months, only CDKN2A/2B biallelic deletion strongly correlates (FDR p.value < 0.01) to a poor outcome in the entire cohort (4y PFS = 44% [32-61] respectively vs. 74% [66-82] for patients in germline configuration; 4y OS = 53% [39-72] vs 83% [76-90]). In a Cox proportional hazard prediction of the PFS, CDKN2A/2B deletion remains predictive (HR = 1.9 [1.1-3.2], p = 0.02) when combined with IPI (HR = 2.4 [1.4-4.1], p = 0.001) and GCB status (HR = 1.3 [0.8-2.3], p = 0.31). This difference remains predictive in the subgroup of patients treated by R-CHOP (4y PFS = 43% [29-63] vs. 66% [55-78], p=0.02), in patients treated by R-ACVBP (4y PFS = 49% [28-84] vs. 83% [74-92], p=0.003), and in GCB (4y PFS = 50% [27-93] vs. 81% [73-90], p=0.02), or ABC/unclassified (5y PFS = 42% [28-61] vs. 67% [55-82] p = 0.009) molecular subtypes (Figure 1). Conclusion: We report for the first time an integrated genetic analysis of a large cohort of DLBCL patients included in a prospective multicentric clinical trial program allowing identifying new potential driver genes with pathogenic impact. However CDKN2A/2B deletion constitutes the strongest and unique prognostic factor of chemoresistance to R-CHOP, regardless the COO signature, which is not overcome by a more intensified immunochemotherapy. Patients displaying this frequent genomic abnormality warrant new and dedicated therapeutic approaches.

Adaptation to marginal habitats

The ability to adapt to marginal habitats, in which survival and reproduction are initially poor, plays a crucial role in the evolution of ecological niches and species ranges. Adaptation to marginal habitats may be limited by genetic, developmental, and functional constraints, but also by consequences of demographic characteristics of marginal populations. Marginal populations are often sparse, fragmented, prone to local extinctions, or are demographic sinks subject to high immigration from high-quality core habitats. This makes them demographically and genetically dependent on core habitats and prone to gene flow counteracting local selection. Theoretical and empirical research in the past decade has advanced our understanding of conditions that favor adaptation to marginal habitats despite those limitations. This review is an attempt at synthesis of those developments and of the emerging conceptual framework.

DNA methylation profiles of human active and inactive X chromosomes.

X-chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. To characterize epigenetic changes that accompany this process, we measured DNA methylation levels in 45,X patients carrying a single active X chromosome (X(a)), and in normal females, who carry one X(a) and one inactive X (X(i)). Methylated DNA was immunoprecipitated and hybridized to high-density oligonucleotide arrays covering the X chromosome, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands (CGIs). While the majority of CGIs show increased methylation levels on the X(i), XCI actually results in significant reductions in methylation at 7% of CGIs. Both intra- and inter-genic CGIs undergo epigenetic modification, with the biggest increase in methylation occurring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI generally have low levels of promoter methylation, while genes that show inter-individual variation in silencing show intermediate increases in methylation. Thus, promoter methylation and susceptibility to XCI are correlated. We also observed a global correlation between CGI methylation and the evolutionary age of X-chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We used our epigenetic map to predict 26 novel genes escaping XCI, and searched for parent-of-origin-specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides a detailed analysis of the epigenetic profile of active and inactive X chromosomes.

Novel methods improve prediction of species' distributions from occurrence data

Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

Moesin interacts with the cytoplasmic region of intercellular adhesion molecule-3 and is redistributed to the uropod of T Lymphocytes during cell polarization

During activation, T lymphocytes become motile cells, switching from a spherical to a polarized shape. Chemokines and other chemotactic cytokines induce lymphocyte polarization with the formation of a uropod in the rear pole, where the adhesion receptors intercellular adhesion molecule-1 (ICAM-1), ICAM-3, and CD44 redistribute. We have investigated membrane-cytoskeleton interactions that play a key role in the redistribution of adhesion receptors to the uropod. Immunofluorescence analysis showed that the ERM proteins radixin and moesin localized to the uropod of human T lymphoblasts treated with the chemokine RANTES (regulated on activation, normal T cell expressed, and secreted), a polarization-inducing agent; radixin colocalized with arrays of myosin II at the neck of the uropods, whereas moesin decorated the most distal part of the uropod and colocalized with ICAM-1, ICAM-3, and CD44 molecules. Two other cytoskeletal proteins, ß-actin and ¿-tubulin, clustered at the cell leading edge and uropod, respectively, of polarized lymphocytes. Biochemical analysis showed that moesin coimmunoprecipitates with ICAM-3 in T lymphoblasts stimulated with either RANTES or the polarization- inducing anti-ICAM-3 HP2/19 mAb, as well as in the constitutively polarized T cell line HSB-2. In addition, moesin is associated with CD44, but not with ICAM-1, in polarized T lymphocytes. A correlation between the degree of moesin-ICAM-3 interaction and cell polarization was found as determined by immunofluorescence and immunoprecipitation analysis done in parallel. The moesin-ICAM-3 interaction was specifically mediated by the cytoplasmic domain of ICAM-3 as revealed by precipitation of moesin with a GST fusion protein containing the ICAM-3 cytoplasmic tail from metabolically labeled Jurkat T cell lysates. The interaction of moesin with ICAM-3 was greatly diminished when RANTES-stimulated T lymphoblasts were pretreated with the myosin-disrupting drug butanedione monoxime, which prevents lymphocyte polarization. Altogether, these data indicate that moesin interacts with ICAM-3 and CD44 adhesion molecules in uropods of polarized T cells; these data also suggest that these interactions participate in the formation of links between membrane receptors and the cytoskeleton, thereby regulating morphological changes during cell locomotion.

Not all inflammatory markers are linked to kidney function: results from a population-based study.

BACKGROUND: Several studies have reported increased levels of inflammatory biomarkers in chronic kidney disease (CKD), but data from the general population are sparse. In this study, we assessed levels of the inflammatory markers C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), interleukin (IL)-1β and IL-6 across all ranges of renal function. METHODS: We conducted a cross-sectional study in a random sample of 6,184 Caucasian subjects aged 35-75 years in Lausanne, Switzerland. Serum levels of hsCRP, TNF-α, IL-6, and IL-1β were measured in 6,067 participants (98.1%); serum creatinine-based estimated glomerular filtration rate (eGFR(creat), CKD-EPI formula) was used to assess renal function, and albumin/creatinine ratio on spot morning urine to assess microalbuminuria (MAU). RESULTS: Higher serum levels of IL-6, TNF-α and hsCRP and lower levels of IL-1β were associated with a lower renal function, CKD (eGFR(creat) <60 ml/min/1.73 m(2); n = 283), and MAU (n = 583). In multivariate linear regression analysis adjusted for age, sex, hypertension, smoking, diabetes, body mass index, lipids, antihypertensive and hypolipemic therapy, only log-transformed TNF-α remained independently associated with lower renal function (β -0.54 ±0.19). In multivariate logistic regression analysis, higher TNF-α levels were associated with CKD (OR 1.17; 95% CI 1.01-1.35), whereas higher levels of IL-6 (OR 1.09; 95% CI 1.02-1.16) and hsCRP (OR 1.21; 95% CI 1.10-1.32) were associated with MAU. CONCLUSION: We did not confirm a significant association between renal function and IL-6, IL-1β and hsCRP in the general population. However, our results demonstrate a significant association between TNF-α and renal function, suggesting a potential link between inflammation and the development of CKD. These data also confirm the association between MAU and inflammation.

Applicability of a distributed watershed pollution model in a data-poor environment in Santa Catarina State, Brazil

Intensification of agricultural production without a sound management and regulations can lead to severe environmental problems, as in Western Santa Catarina State, Brazil, where intensive swine production has caused large accumulations of manure and consequently water pollution. Natural resource scientists are asked by decision-makers for advice on management and regulatory decisions. Distributed environmental models are useful tools, since they can be used to explore consequences of various management practices. However, in many areas of the world, quantitative data for model calibration and validation are lacking. The data-intensive distributed environmental model AgNPS was applied in a data-poor environment, the upper catchment (2,520 ha) of the Ariranhazinho River, near the city of Seara, in Santa Catarina State. Steps included data preparation, cell size selection, sensitivity analysis, model calibration and application to different management scenarios. The model was calibrated based on a best guess for model parameters and on a pragmatic sensitivity analysis. The parameters were adjusted to match model outputs (runoff volume, peak runoff rate and sediment concentration) closely with the sparse observed data. A modelling grid cell resolution of 150 m adduced appropriate and computer-fit results. The rainfall runoff response of the AgNPS model was calibrated using three separate rainfall ranges (< 25, 25-60, > 60 mm). Predicted sediment concentrations were consistently six to ten times higher than observed, probably due to sediment trapping along vegetated channel banks. Predicted N and P concentrations in stream water ranged from just below to well above regulatory norms. Expert knowledge of the area, in addition to experience reported in the literature, was able to compensate in part for limited calibration data. Several scenarios (actual, recommended and excessive manure applications, and point source pollution from swine operations) could be compared by the model, using a relative ranking rather than quantitative predictions.

Enhancement of the photoelectrochemical properties of Cl-doped ZnO nanowires by tuning their coaxial doping profile

Arrays of vertically aligned ZnO:Cl/ZnO core-shell nanowires were used to demonstrate that the control of the coaxial doping profile in homojunction nanostructures can improve their surface charge carrier transfer while conserving potentially excellent transport properties. It is experimentally shown that the presence of a ZnO shell enhances the photoelectrochemical properties of ZnO:Cl nanowires up to a factor 5. Likewise, the ZnO shell promotes the visible photoluminescence band in highly conducting ZnO:Cl nanowires. These lines of evidence are associated with the increase of the nanowires" surface depletion layer