The DNA polymerase λ is required for the repair of non-compatible DNA double strand breaks by NHEJ in mammalian cells

DNA polymerase lambda (polλ) is a recently identified DNA polymerase whose cellular function remains elusive. Here we show, that polλ participates at the molecular level in a chromosomal context, in the repair of DNA double strand breaks (DSB) via non-homologous end joining (NHEJ) in mammalian cells. The expression of a catalytically inactive form of polλ (polλDN) decreases the frequency of NHEJ events in response to I-Sce-I-induced DSB whereas inactivated forms of its homologues polβ and polμ do not. Only events requiring DNA end processing before ligation are affected; this defect is associated with large deletions arising in the vicinity of the induced DSB. Furthermore, polλDN-expressing cells exhibit increased sensitization and genomic instability in response to ionizing radiation similar to that of NHEJ-defective cells. Our data support a requirement for polλ in repairing a subset of DSB in genomic DNA, thereby contributing to the maintenance of genetic stability mediated by the NHEJ pathway

Traitement des eaux résiduaires de temps sec et temps de pluie en réseau unitaire par filtres plantés de roseaux

Les filtres plantés de roseaux à écoulement vertical (FPR-V) pour le traitement des eaux usées domestiques sont relativement bien développés en France et permettent de réaliser un traitement poussé de la matière carbonée et la nitrification. La robustesse de cette filière réside également dans sa capacité à accepter des surcharges hydrauliques en temps de pluie. Cependant ces limites d acceptation hydraulique ne sont pas bien définies et demandent à être optimisées. La conception des FPR-V pour accepter des surcharges hydrauliques est un travail complexe car le contexte local affecte fortement les débits d eau entrants dans la station lors d un événement pluvieux. Dans de tels cas, la conception de filtres demande l utilisation de modèles dynamiques. Ces modèles s appuient le plus souvent sur une approche mécanistique et sont à l'origine conçus et utilisés pour la recherche. Cependant, si ces modèles sont des outils puissants pour décrire en détail la dynamique du FPR-V, ils sont généralement trop complexes à manipuler pour des utilisateurs non experts. Choisir entre une description détaillée et une manipulation facile dépendra des objectifs de modélisation. Quand des objectifs de dimensionnement global sont visés par les concepteurs, l'utilisation de modèles simplifiés semble une bonne alternative. Les modèles simplifiés sont faciles à utiliser pour la conception de FPR-V mais ils sont peu nombreux. Cependant ils sont adaptés à des configurations spécifiques liées au traitement des surverses de déversoirs d orage, ce qui n est pas le cas pour les FPR-V traitant des eaux usées domestiques. En effet, pour ce type de FPR-V les vitesses d infiltration du système varient considérablement. En conséquence, ce travail de thèse a pour objectif de développer un modèle hydraulique simplifié des FPR-V qui permettra de guider les concepteurs dans le processus d adaptation des FPR-V pour traiter les eaux usées domestiques des périodes de temps sec et de temps de pluie. Le modèle simplifié permet de relier (i) l hydraulique du filtre, en simulant le temps de noyage à la surface, et (ii) les performances biologiques, en établissant des alertes de dysfonctionnement , basées sur l'évaluation des performances épuratoires et sur les variations des formes azotées à la sortie du filtre mesurées en continu. Les alertes de dysfonctionnement représentent la charge hydraulique maximale qu'un filtre peut accepter sans compromettre son activité biologique. Le modèle simplifié a été utilisé pour la modélisation hydraulique du FPR-V à long terme (i) pour analyser l impact du contexte local et la conception du filtre dans l acceptation de surcharges hydrauliques. Grâce à cet analyse, (ii) on peut proposer les dimensionnements de FPR-V qui arrivent à mieux gérer l acceptation des surcharges hydrauliques.French vertical-flow constructed wetlands (VFCW) directly treating raw wastewater are known to perform well on for SS, COD and nitrification. They are also known to robustly cope with hydraulic overloads during rainfall events. Although numerous systems have been installed in areas equipped with a combined sewer, the limits of stormwater acceptance remain ill-defined and need to be improved. Looking at the various VFCW designs and usages reported in the literature, it is difficult to draw any consensus on their hydraulic limits. Consequently, designing VFCW to accept hydraulic overloads is a complex task, as local context strongly impacts inlet flows produced during rainfall events. Dynamic models appear a requisite for filter design in such cases. Numerical CW models have essentially focused on horizontal flow, with few attempting to study VFCW dynamics which are more commonly tackled via mechanistic models. Although mechanistic models are powerful tools for describing processes within the VFCW, they are generally too complicated to be readily used by designers. The choice between detailed description and easy handling will depend on the modelling aims. If the aim is a global design tool, simplified models offer a good alternative. However, the simplified models geared to studying VFCW dynamics are extremely reduced. They are easy-handling for design and well-adapted to specific purposes (combined sewer overflow -CSO- treatment) but not necessarily to VFCW treating combined sewer wastewater, where long-term infiltration rates vary significantly. Consequently, this PhD thesis work focused on developing a simplified hydraulic model of VFCW to guide designers through the process of adapting VFCW systems to treat domestic wastewater in both dry and rain events. The simplified model makes it possible to link (i) hydraulics, by simulation of ponding time variations, (ii) biological performances, by establishing dysfunction alerts based on treatment performance assessment and variations in online N forms effluent from the young VFCW. These dysfunction alerts plot the maximal hydraulic load that a filter can accept without compromising its biological activity. The simplified model was used to model long-term hydraulics in the VFCW (i) to analyze the impact of local context and filter design on hydraulic overload acceptance (using dysfunction alerts and bypass discharges) and (ii) to propose VFCW designs for accepting hydraulic overload in different contexts. The modelling demonstrates that VFCW can limit days with bypass discharges to less than 20 times per year without jeopardizing filter performances. Moreover, the most problematic scenario on stormwater treatment remains a watershed with high imperviousness coefficient and low slope under a Bretagne-type climate, demonstrating that the filter is more sensitive to periodicity and duration than to intensity of rainfall events.VILLEURBANNE-DOC'INSA-Bib. elec. (692669901) / SudocSudocFranceF

CAROLS: A New Airborne L-Band Radiometer for Ocean Surface and Land Observations

The “Cooperative Airborne Radiometer for Ocean and Land Studies” (CAROLS) L-Band radiometer was designed and built as a copy of the EMIRAD II radiometer constructed by the Technical University of Denmark team. It is a fully polarimetric and direct sampling correlation radiometer. It is installed on board a dedicated French ATR42 research aircraft, in conjunction with other airborne instruments (C-Band scatterometer—STORM, the GOLD-RTR GPS system, the infrared CIMEL radiometer and a visible wavelength camera). Following initial laboratory qualifications, three airborne campaigns involving 21 flights were carried out over South West France, the Valencia site and the Bay of Biscay (Atlantic Ocean) in 2007, 2008 and 2009, in coordination with in situ field campaigns. In order to validate the CAROLS data, various aircraft flight patterns and maneuvers were implemented, including straight horizontal flights, circular flights, wing and nose wags over the ocean. Analysis of the first two campaigns in 2007 and 2008 leads us to improve the CAROLS radiometer regarding isolation between channels and filter bandwidth. After implementation of these improvements, results show that the instrument is conforming to specification and is a useful tool for Soil Moisture and Ocean Salinity (SMOS) satellite validation as well as for specific studies on surface soil moisture or ocean salinity

Digital expression profiling of novel diatom transcripts provides insight into their biological functions

Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance

An introduction to the Digital Observatory for Protected Areas (DOPA) and the DOPA Explorer (Beta)

The Digital Observatory for Protected Areas (DOPA) is conceived around a set of interacting Critical Biodiversity Informatics Infrastructures (databases, web modelling services, broadcasting services, ...) hosted at different institutions, including the Joint Research Centre of the European Commission, the World Conservation Monitoring Centre (UNEP-WCMC), the International Union for Conservation of Nature (IUCN), the Global Biodiversity Information Facility (GBIF) and BirdLife International. The current services of DOPA provide to a large variety of end-users, ranging from park managers, funding agencies to researchers, with means to assess, monitor and possibly forecast the state and pressure of protected areas at the local, national and global scales. With an introduction to the DOPA, the readers will find here a user manual of the beta version of DOPA Explorer, a first web based assessment tool where information on 9 000 protected areas covering almost 90% of the global protected surface has been processed automatically to generate a set of indicators on ecosystems, climate, phenology, species, ecosystem services and pressures. DOPA Explorer can so help identify the protected areas with most unique ecosystems and species and assess the pressures they are exposed to because of human development. Ecological data derived from and near real-time earth observations are also made available for the African continent. Inversely, DOPA Explorer indirectly highlights the protected areas for which the information is incomplete.JRC.H.5-Land Resources Managemen

Involvement of DNA polymerase μ in the repair of a specific subset of DNA double-strand breaks in mammalian cells

The repair of DNA double-strand breaks (DSB) requires processing of the broken ends to complete the ligation process. Recently, it has been shown that DNA polymerase μ (polμ) and DNA polymerase λ (polλ) are both involved in such processing during non-homologous end joining in vitro. However, no phenotype was observed in animal models defective for either polμ and/or polλ. Such observations could result from a functional redundancy shared by the X family of DNA polymerases. To avoid such redundancy and to clarify the role of polμ in the end joining process, we generated cells over-expressing the wild type as well as an inactive form of polμ (polμD). We observed that cell sensitivity to ionizing radiation (IR) was increased when either polμ or polμD was over-expressed. However, the genetic instability in response to IR increased only in cells expressing polμD. Moreover, analysis of intrachromosomal repair of the I-SceI-induced DNA DSB, did not reveal any effect of either polμ or polμD expression on the efficiency of ligation of both cohesive and partially complementary ends. Finally, the sequences of the repaired ends were specifically affected when polμ or polμD was over-expressed, supporting the hypothesis that polμ could be involved in the repair of a DSB subset when resolution of junctions requires some gap filling

Safety and Efficacy of Nivolumab Monotherapy in Recurrent or Metastatic Cervical, Vaginal, or Vulvar Carcinoma: Results From the Phase I/II CheckMate 358 Trial

Purpose: Nivolumab was assessed in patients with virus-associated tumors in the phase I/II CheckMate 358 trial (ClinicalTrials.gov identifier: NCT02488759). We report on patients with recurrent/metastatic cervical, vaginal, or vulvar cancers. Patients and methods: Patients received nivolumab 240 mg every 2 weeks. Although patients with unknown human papillomavirus status were enrolled, patients known to have human papillomavirus-negative tumors were ineligible. The primary end point was objective response rate. Duration of response (DOR), progression-free survival, and overall survival were secondary end points. Safety and patient-reported outcomes were exploratory end points. Results: Twenty-four patients (cervical, n = 19; vaginal/vulvar, n = 5) were enrolled. Most patients had received prior systemic therapy for metastatic disease (cervical, 78.9%; vaginal/vulvar, 80.0%). Objective response rates were 26.3% (95% CI, 9.1 to 51.2) for cervical cancer and 20.0% (95% CI, 0.5 to 71.6) for vaginal/vulvar cancers. At a median follow-up of 19.2 months, median DOR was not reached (range, 23.3 to 29.5+ months; + indicates a censored observation) in the five responding patients in the cervical cohort; the DOR was 5.0 months in the single responding patient in the vaginal/vulvar cohort. Median overall survival was 21.9 months (95% CI, 15.1 months to not reached) among patients with cervical cancer. Any-grade treatment-related adverse events were reported in 12 of 19 patients (63.2%) in the cervical cohort and all five patients in the vaginal/vulvar cohort; there were no treatment-related deaths. In the cervical cohort, nivolumab treatment generally resulted in stabilization of patient-reported outcomes associated with health status and health-related quality of life. Conclusion: The efficacy of nivolumab in patients with recurrent/metastatic cervical and vaginal or vulvar cancers is promising and warrants additional investigation. No new safety signals were identified with nivolumab treatment in this population

Détermination du débit de filtration glomérulaire au cours de la drépanocytose au Sénégal: Schwartz, Cockcroft et Gault, MDRD, CKD-EPI ou JSCCS ?

La détermination du Débit de Filtration Glomérulaire (DFG) est importante chez les drépanocytaires du fait qu’ils constituent un groupe de patients chez lesquels des atteintes rénales sont fréquemment décrites notamment l’hyperfiltration glomérulaire. Dès lors, à une époque où les calculateurs en ligne proposent simultanément différentes formules de détermination du DFG, il serait important d’évaluer au sein d’une population noire africaine drépanocytaire l’équivalence entre ces formules qui ont été développées et validées sur des populations caucasiennes et afro-américaines à DFG normal ou diminué. Ainsi cette étude avait pour but d’évaluer l’interchangeabilité des différentes formules de détermination du DFG en les appliquant à des drépanocytaires. Des enfants et adultes sénégalais drépanocytaires homozygotes ont été alors recrutés et leur DFG calculé. La fréquence de l’hyperfiltration glomérulaire et celle de l’insuffisance rénale ont été calculées à partir des résultats obtenus avec les formules de Schwartz et du CKD-EPI. La concordance des différentes formules a été évaluée avec la méthode Bland-Altman. Au total 56 adultes et 62 enfants ont été inclus dans l’étude. L’insuffisance rénale a été notée chez 1,78% des adultes et 9,68% des enfants ; l’hyperfiltration glomérulaire chez 66,10% des adultes et 25,8% des enfants. Par rapport aux formules de référence (CKD-EPI, Schwartz), tous les biais relevés étaient significativement différents de zéro à l’exception de celui de Cockcroftet Gault qui était statistiquement nul. Les limites de concordance étaient toutes inacceptablement larges par rapport aux limites attendues à l’exception de celles du CKD-EPI sans ajustement sur la race. Ainsi, la formule de Schwartz n’était pas interchangeable avec celle du JSCCS chez les enfants, tout comme celle du CKD-EPI ne l’était pas non plus avec celles du JSCCS, de Cockcroft, du MDRD ou du CKD-EPI sans ajustement sur la race chez les adultes drépanocytaires.   English title: Determination of glomerular filtration rate in sickle cell disease in Senegal: Schwartz, Cockcroft and Gault, MDRD, CKD-EPI or JSCCS? Determination of Glomerular Filtration Rate (GFR) is important in patients living with sickle cell disease (SCD) because they constitute a group of patients where kidney dysfunction is frequently described, in particular glomerular hyperfiltration. Therefore, at a time when online calculators simultaneously propose different formulas to estimate GFR, it would be important to evaluate in a black African population living with SCD the equivalence between these formulas which have been developed and validated on Caucasian and African American populations with normal or decreased GFR. Thus, the aim of this study was to evaluate interchangeability of different GFR formulas in a group of patients living with SCD. Homozygous Senegalese sickle cell children and adults were then recruited and their GFR computed using Schwartz and JSCCS in children, Cockcroft and Gault, CKD-EPI with and without adjustment for ethnicity, MDRD and JSCCS formulas in adults. The frequency of glomerular hyperfiltration and renal failure was computed based on the results generated using Schwartz and CKD-EPI formulas. The agreement between formulas was assessed with BlandAltman method. A total of 56 adults and 62 children were included in this study. Renal failure was observed in 1.78% of adults and 9.68% of children; glomerular hyperfiltration in 66.10% of adults and 25.8% of children. Compared with reference formulas (CKD-EPI, Schwartz), all biases found were significantly different from zero except for Cockcroft and Gault formula bias, which was statistically zero. The limits of agreement were all unacceptably wide compared with the expected limits with the exception of CKD-EPI without adjustment for ethnicity. Thus, Schwartz formula would not be interchangeable with JSCCS formula in children, nor was the CKD-EPI formula interchangeable with the JSCCS, Cockcroft and Gault, MDRD or CKD-EPI without adjustment for ethnicity formulas in adults living with sickle cell anemia