Guidelines for the use and interpretation of assays for monitoring autophagy.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.

A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also "genome regulation." Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype.

Des personnages érigés en narrateurs : les voix over chez Joseph L. Mankiewicz (A Letter to Three Wives, All about Eve et The Barefoot Contessa). Pour une approche énonciative du récit filmique

L'auteur analyse dans une perspective narratologique trois films de Joseph L. Mankiewicz réalisés entre 1949 et 1954 (A Letter to Three Wives, All about Eve et The Barefoot Contessa), afin d'observer les particularités qui résultent du recours à un ou plusieurs narrateurs (ou narratrices) s'exprimant en voix over. L'accent est mis sur les implications de l'organisation énonciative complexe de ces productions cinématographiques en termes de relation du film au spectateur et de représentation des rapports de genre. Ces études de cas permettent de nuancer certains acquis issus du champ des théories de l'énonciation. Dans ces films où les voix over sont proférées par des acteurs qui incarnent par ailleurs un personnage visualisé, certaines interactions sont observables - interprétées notamment comme des relations de pouvoir - entre le statut des narrateurs et le niveau diégétique. La matérialité sonore est prise en compte dans le cas particulier de Letter to Three Wives, où la voix se transforme en bruit. Cet « effet spécial » est l'occasion de discuter un modèle « impersonnel » de l'énonciation filmique qui intègre, tout en tenant compte de la dimension technologique de l'enregistrement sonore, le pouvoir fondamentalement humanisant des manifestations vocales.

A critical edition of Joseph Conrad's "Because of the dollars" (Within the Tides, 1915)

Cette thèse de doctorat, écrite en anglais, propose la première édition critique de « Because of the Dollars », une nouvelle de l'écrivain anglais Joseph Conrad publiée dans le volume Within the Tides, en février 1915. Outre le texte critique de la nouvelle - le seul à ce jour reconstruit d'après une minutieuse étude des relations entre toutes les versions existantes - la présente édition offre aussi un vaste apparat éditorial. Le texte de la présente édition est éclectique. Sa ponctuation est essentiellement basée sur un texte proche du manuscrit de l'auteur, et donc non corrompu par le processus de transmission. Mais ses mots sont tirés des dernières versions révisées par l'auteur, étant donné qu'au cours de la transmission, les mots, contrairement aux marques de ponctuation, n'ont pas été contaminés. Le résultat de cette méthode est un texte reflétant, tant pour les mots que pour la ponctuation, les choix de l'auteur. L'apparat éditorial sert à placer la nouvelle dans la vie de Conrad, tracer l'évolution du texte, et offrir au lecteur des informations historiques et culturelles qui permettront une meilleure lecture de l'oeuvre. Cet apparat est composé de quatre parties : une introduction, une étude sur les textes de la nouvelle, une collation historique de toutes les variantes, et des notes explicatives. L'introduction place l'oeuvre dans le contexte de la vie de l'écrivain, en donne la réception critique de 1915 à nos jours, et en éclaire le contexte historique (un changement de monnaie à Singapour en 1903-4). L'étude sur les textes trace le développement et la transmission du texte, depuis son inscription sur pages manuscrites jusqu'à sa publication dans les oeuvres complètes de Conrad. La collation historique inventorie toutes les variantes textuelles entre les différentes versions existantes. Enfin, les notes explicatives glosent les allusions littéraires, historiques, et culturelles du texte. « Because of the Dollars » et Within the Tides n'ayant attiré que très peu d'attention critique, les informations contenues dans cet apparat éditorial sont complètement inédites, et jettent une lumière originale sur une période peu étudiée de la vie de Conrad.

Male dominance linked to size and age, but not to 'good genes' in brown trout (Salmo trutta).

BACKGROUND: Males that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolise most mates and sire most offspring. We drew a random sample of mature male brown trout (Salmo trutta) from two wild populations and determined their dominance hierarchy or traits linked to dominance. The fish were then stripped and their sperm was used for in vitro fertilisations in two full-factorial breeding designs. We recorded embryo viability until hatching in both experiments, and juvenile survival during 20 months after release into a natural streamlet in the second experiment. Since offspring of brown trout get only genes from their fathers, we used offspring survival as a quality measure to test (i) whether males differ in their genetic quality, and if so, (ii) whether dominance or traits linked to dominance reveal 'good genes'. RESULTS: We found significant additive genetic variance on embryo survival, i.e. males differed in their genetic quality. Older, heavier and larger males were more successful in intra-sexual selection. However, neither dominance nor dominance indicators like body length, weight or age were significantly linked to genetic quality measured as embryo or juvenile survival. CONCLUSION: We found no evidence that females can improve their offspring's genetic viability by mating with large and dominant males. If there still were advantages of mating with dominant males, they may be linked to non-genetic benefits or to genetic advantages that are context dependent and therefore possibly not revealed under our experimental conditions - even if we found significant additive genetic variation for embryo viability under such conditions.

Effects of different mating scenarios on embryo viability in brown trout.

Mating with attractive or dominant males is often predicted to offer indirect genetic benefits to females, but it is still largely unclear how important such non-random mating can be with regard to embryo viability. We sampled a natural population of adult migratory brown trout (Salmo trutta), bred them in vitro in a half-sib breeding design to separate genetic from maternal environmental effects, raised 2098 embryos singly until hatching, and exposed them experimentally to different levels of pathogen stress at a late embryonic stage. We found that the embryos' tolerance to the induced pathogen stress was linked to the major histocompatibility complex (MHC) of their parents, i.e. certain MHC genotypes appeared to provide better protection against infection than others. We also found significant additive genetic variance for stress tolerance. Melanin-based dark skin patterns revealed males with 'good genes', i.e. embryos fathered by dark coloured males had a high tolerance to infection. Mating with large and dominant males would, however, not improve embryo viability when compared to random mating. We used simulations to provide estimates of how mate choice based on MHC or melanin-based skin patterns would influence embryos' tolerance to the experimentally induced pathogen stress.

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Immunoelectron microscopical identification of the uncoupling protein in brown adipose tissue mitochondria.

The distribution of the uncoupling protein (UCP) in brown adipocyte mitochondria of the hibernant Muscardinus avellanarius was obtained by ultrastructural immunocytochemistry. In both cryosections and sections of Lowicryl-embedded material UCP was localized in the mitochondrial cristae of brown adipocytes, but not in liver mitochondria. It should now be possible to easily identify the morphology of cells committed to BAT differentiation in the tissue as well as in cell culture.

L'usage du narratif dans le Testament de Joseph

(Résumé de l'ouvrage) Seventeen innovative studies are collected in this volume which has been produced under the aegis of the Centre for Biblical Studies, University of Manchester, and L'Institut des sciences bibliques, Université de Lausanne. The majority of the studies engage with narrative through providing insightful working examples. Building on the many contributions of recent narratological research, for the most part the studies in this collection avoid the technical language of narratology as they present fresh insights at many levels. Some essays focus more on the implied author, some on the implied reader or hearer, and some on the way particular messages are constructed; some of the studies consider how author, message and reader are all interconnected. There are several creative proposals for refining genre definition, from law and wisdom to gospel and apocryphal writings. Some studies highlight the way in which narratives can contain ethical, religious, and cultural messages. Sensitivity to narrative is also shown by some contributors to expose in intruing ways the redactional processes behind the final form of texts. Students of narrative in the ancient world will find much to consider in this book, and others engaged with literary studies more generally will discover that scholars of the worlds of the Bible and Late Antiquity have much to offer them.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Le Messie, fils de Joseph

(Résumé de l'ouvrage) Vrai ou faux, attendu ou advenu, réel ou supposé, le Messie sous ses multiples figures traverse notre histoire, façonnant nos univers religieux et culturels. Vingt chercheurs, venus de différentes disciplines, confrontent leurs analyses sur les origines de cette idée, sa prégnance, et les transformations qu'elle a connues jusqu'à nos jours. Quelle place la figure du Messie occupe-t-elle dans le judaïsme, le christianisme et l'islamisme ? Comment l'idée de Messie a-t-elle fécondé l'ensemble de notre univers culturel ? Telles sont quelques-unes des pistes explorées par cet ouvrage.

Six years of denosumab treatment in postmenopausal women with osteoporosis: results from the first three years of the freedom extension

Background/Purpose: Denosumab (DMAb) is an approved therapy for the treatment of postmenopausal women with osteoporosis at increased risk for fracture. A favorable risk/benefit profile was demonstrated in the pivotal, 3-year FREEDOM trial (Cummings et al NEJM 2009). The open-label, active-treatment FREEDOM Extension study is investigating the efficacy and safety of DMAb for up to 10 years. The Extension trial enrolled women who had received DMAb or placebo in FREEDOM and provides an opportunity to evaluate the long-term efficacy and safety of continuous DMAb treatment (long-term group), and to replicate the DMAb findings observed in FREEDOM (cross-over group). Here, we report the results from the first 3 years of the Extension, representing up to 6 continuous years of DMAb exposure.Methods: During the Extension, each woman is scheduled to receive 60 mg DMAb every 6 months and supplemental calcium and vitamin D daily. For the analyses reported here, women from the FREEDOM DMAb group received 3 more years of DMAb for a total of 6 years of exposure (long-term group) and women from the FREEDOM placebo group received 3 years of DMAb exposure (cross-over group).Results: Of the 5928 women eligible for the Extension, 4550 (77%) enrolled (N_2343 long-term; N_2207 cross-over). In the long-term group, further significant mean increases in bone mineral density (BMD) occurred 4044 for cumulative 6-year gains of 15.2% at the lumbar spine and 7.5% at the total hip (Figure). During the first 3 years of DMAb treatment during the Extension, the cross-over group had significant mean gains in BMD at the lumbar spine (9.4%) and total hip (4.8%), similar to those observed in the long-term DMAb group during the first 3 years of FREEDOM (lumbar spine, 10.1%; total hip, 5.7%). Serum CTX was rapidly and similarly reduced after the 1st (cross-over) or 7th (long-term) DMAb dose with the characteristic attenuation observed at the end of the dosing period. In the cross-over group, yearly incidences of new vertebral and nonvertebral fractures were lower than in the FREEDOM placebo group. Fracture incidence remained low in the long-term group. Incidences of adverse events (AEs) and serious AEs did not increase over time with DMAb treatment. There were 2 subjects with AEs adjudicated to ONJ in the cross-over group and 2 in the long-term group. Both cases in the cross-over group healed completely and without further complications; 1 of these subjects continues to receive DMAb. Both women in the long-term group continue to be followed. No atypical femur fractures have been observed to date. Figure. Percent changes in bone mineral density during FREEDOM and the Extension Conclusion: DMAb treatment for 6 continuous years (long-term group) remained well tolerated, maintained reduced bone turnover, and continued to significantly increase BMD. Fracture incidence remained low. DMAb treatment for 3 years in the cross-over group reproduced the original observations in FREEDOM.

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.

Blood pressure is a heritable trait influenced by several biological pathways and responsive to environmental stimuli. Over one billion people worldwide have hypertension (≥140 mm Hg systolic blood pressure or  ≥90 mm Hg diastolic blood pressure). Even small increments in blood pressure are associated with an increased risk of cardiovascular events. This genome-wide association study of systolic and diastolic blood pressure, which used a multi-stage design in 200,000 individuals of European descent, identified sixteen novel loci: six of these loci contain genes previously known or suspected to regulate blood pressure (GUCY1A3-GUCY1B3, NPR3-C5orf23, ADM, FURIN-FES, GOSR2, GNAS-EDN3); the other ten provide new clues to blood pressure physiology. A genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke and coronary artery disease, but not kidney disease or kidney function. We also observed associations with blood pressure in East Asian, South Asian and African ancestry individuals. Our findings provide new insights into the genetics and biology of blood pressure, and suggest potential novel therapeutic pathways for cardiovascular disease prevention.