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Supplemental Tables S1-S3. Table S1 describes the antiproliferative activity of SAR125844 on a panel of cell lines and the known genetic alterations of MET and other oncogenes or tumor suppressor genes for these cell lines. Table S2 describes the antiproliferative activity of SAR125844 upon various times of exposure in Hs 746T MET-amplified tumor cell line. Table S3 describes tumor exposure over plasma exposure ratios for SAR125844, JNJ-38877605 and PF-04217903 MET inhibitors.

Supplementary Figure S2

Purpose:Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) is a glycoprotein that has limited expression in normal adult tissues, but is overexpressed in carcinomas of the gastrointestinal tract, the genitourinary and respiratory systems, and breast cancer. As such, CEACAM5 is an attractive target for antibody-based therapies designed to selectively deliver cytotoxic drugs to certain epithelial tumors. Here, we describe preclinical data for a novel antibody–drug conjugate (ADC), SAR408701, which consists of an anti-CEACAM5 antibody (SAR408377) coupled to a maytansinoid agent DM4 via a cleavable linker.Experimental Design:The specificity and binding affinity of SAR408701 to human and cynomolgus monkey CEACAM5 were tested in vitro. The cytotoxic activity of SAR408701 was assessed in CEACAM5-expressing tumor cell lines and using patient-derived xenograft mouse models of CEACAM5-positive tumors. Pharmacokinetic-pharmacodynamic and pharmacokinetic-efficacy relationships were established. SAR408701 toxicity was evaluated in cynomolgus monkey.Results:SAR408701 bound selectively to human and cynomolgus monkey CEACAM5 with similar apparent Kd values (0.017 nmol/L and 0.024 nmol/L, respectively). Both in vitro and in vivo evaluations showed that SAR408701 has cytotoxic activity, leading to in vivo efficacy in single and repeated dosing. Single doses of SAR408701 induced significant increases in the tumor expression of phosphorylated histone H3, confirming the tubulin-targeting mechanism of action. The overall toxicity profile of SAR408701 in cynomolgus monkey was similar to that observed after intravenous administration of DM4 alone.Conclusions:On the basis of these preclinical data, the ADC SAR408701 is a promising candidate for development as a potential treatment for patients with CEACAM5-positive tumors.

Supplementary Materials

International audience; Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant–fungi–virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assessed the richness, diversity, and composition of leaf‐associated fungal and viral communities from pools of herbaceous wild plants representative of four sites corresponding to cultivated or natural ecosystems. We identified 161 fungal families and 18 viral families comprising 249 RNA‐dependent RNA polymerase‐based operational taxonomic units (RdRp OTUs) from leaves. Fungal culturomics captured 12.3% of the fungal diversity recovered with metagenomic approaches and, unexpectedly, retrieved viral OTUs that were almost entirely different from those recovered by leaf metagenomics. Ecosystem management had a significant influence on both leaf mycobiome and virome, with a higher fungal community richness in natural ecosystems and a higher viral family richness in cultivated ecosystems, suggesting that leaf‐associated fungal and viral communities are under the influence of different ecological drivers. Both the leaf‐associated fungal and viral community compositions showed a strong site‐specificity. Further research is needed to confirm these trends and unravel the factors structuring plant–fungi–virus interactions in wild plant populations.

Introduction Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest.

Aim Heart failure with preserved ejection fraction (HFpEF) is a major cause of death worldwide with no approved treatment. Left ventricular hypertrophy (LVH) and diastolic dysfunction represent the structural and functional components of HFpEF, respectively. Endothelial dysfunction is prevalent in HFpEF and predicts cardiovascular events. We investigated if SAR247799, a G-protein-biased sphingosine-1-phosphate receptor 1 (S1P1) agonist with endothelial-protective properties, could improve cardiac and renal functions in a rat model of metabolic syndrome LVH and diastolic function. Methods 31- and 65-week-old obese ZSF1 (Ob-ZSF1) rats, representing adult and aged animals with LVH and diastolic dysfunction, were randomized to a chow diet containing 0.025% (w/w) of SAR247799, or control (CTRL) chow for 4 weeks. Age-matched lean ZSF1 (Le-ZSF1) rats were fed control chow. Echocardiography, telemetry, biochemical and histological analysis were performed to evaluate the effect of SAR247799. Results Echocardiography revealed that Ob-ZSF1 rats, in contrast to Le-ZSF1 rats, developed progressive diastolic dysfunction and cardiac hypertrophy with age. SAR247799 blunted the progression of diastolic dysfunction in adult and aged animals: in adult animals E/e’ was evaluated at 21.8 ± 1.4 for Ob-ZSF1-CTRL, 19.5 ± 1.2 for Ob-ZSF1-SAR247799 p1 desensitization. Conclusions These experimental findings suggest that S1P1 activation with SAR247799 may be considered as a new therapeutic approach for LVH and diastolic dysfunction, major components of HFpEF.

Background As eating behavior changes in relation to the menstrual cycle and weight changes with menopausal transition, ovarian hormones appear to be involved in regulating eating behavior. However, observations are contradictory and are difficult to compare, due to methodological problems related to nutritional epidemiology. To better understand the relationship between ovarian steroid hormones and eating behavior, our study evaluates women's responses to visual food cues at different points in the menstrual cycle with their specific serum estrogen/progesterone levels and women's responses in the case of strong estrogen changes in the context of fertility treatments. Methods We collected data from 129 women, 44 of whom received in vitro fertilization (IVF) at the Department of Reproductive Endocrinology, University Hospital Zurich. A total of 85 women with natural cycles were recruited at the University Hospital Zurich (n = 37) and at the Hannover Medical School (n = 48). Our observational study used 4 different measurement time points across the natural cycle and 2 measurement time points in women with supraphysiological estradiol levels during fertility treatments. Using a second cycle, we then tested our results for replication. At these predefined time points, women were shown pictures of 11 categories of food, with 4 items for each category and blood samples for measurement of hormone levels were taken. Food preferences registered at the time of the investigation were indicated on a visual analogue scale (0–100). Results We did not find any statistically significant association between women's serum hormone levels and the rating of visually presented food, either during the menstrual cycle or during fertility treatments after controlling for multiple testing (all p > 0.005). Ratings for fruits, vegetables, and carbohydrates showed a significant linear decline throughout the first menstrual cycle (p < 0.01), which did not replicate in the second cycle (p > 0.05). In contrast, the ratings for sweets showed a significant linear decline in both cycles (both p < 0.01), with a mean rating of 54.2 and 48.8 in the menstrual phase of the first and second cycle, respectively, to a mean rating of 47.7 and 43.4 in the premenstrual phase of the first and second cycle, respectively. During fertility treatments, no food rating showed a significant change (all p > 0.05). Mood such as negative and positive affects did not influence ratings for visual food cues neither throughout the menstrual cycles nor during fertility treatment. Conclusions Serum levels of estradiol and progesterone do not correlate with food ratings in women, even when estradiol levels are above the physiological level of a natural menstrual cycle. Since, except for sweets, significant changes in food ratings in a first cycle did not replicate in a second menstrual cycle, significant findings from the literature based on animal or human studies focusing on a single-cycle have to be interpreted with caution. publishedVersion

RecommendationEmmanuelle Lerat (2021) A new tool to cross and analyze TE and gene annotations. Peer Community inGenomics, 100010. 10.24072/pci.genomics.100010Transposable elements (TEs) are important components of genomes. Indeed, they are now recognized as having a major role in gene and genome evolution (Biémont 2010). In particular, several examples have shown that the presence of TEs near genes may influence their functioning, either by recruiting particular epigenetic modifications (Guio et al. 2018) or by directly providing new regulatory sequences allowing new expression patterns (Chung et al. 2007; Sundaram et al. 2014). Therefore, the study of the interaction between TEs and their host genome requires tools to easily cross-annotate both types of entities. In particular, one needs to be able to identify all TEs located in the close vicinity of genes or inside them. Such task may not always be obvious for many biologists, as it requires informatics knowledge to develop their own script codes.In their work, Meguerdichian et al. (2021) propose a command-line pipeline that takes as input the annotations of both genes and TEs for a given genome, then detects and reports the positional relationships between each TE insertion and their closest genes. The results are processed into an R script to provide tables displaying some statistics and graphs to visualize these relationships. This tool has the potential to be very useful for performing preliminary analyses before studying the impact of TEs on gene functioning, especially for biologists. Indeed, it makes it possible to identify genes close to TE insertions. These identified genes could then be specifically considered in order to study in more detail the link between the presence of TEs and their functioning. For example, the identification of TEs close to genes may allow to determine their potential role on gene expression.; Understanding the relationship between transposable elements (TEs) and their closest positional genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural organization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline.

Viral metagenomics relies on high-throughput sequencing and on bioinformatic analyses to access the genetic content and diversity of entire viral communities. No universally accepted strategy or tool currently exists to define operational taxonomy units (OTUs) and evaluate viral alpha or beta diversity from virome data. Here we present a new bioinformatic resource, the VirAnnot (automated viral diversity estimation) pipeline, which performs the automated identification of OTUs. Reverse-position-specific BLAST (RPS-Blastn) is used to detect conserved viral protein motifs. The corresponding contigs are then aligned and a clustering approach is used to group in the same OTU contigs sharing more than a set identity threshold. A 10% threshold has been validated as producing OTUs that reasonably approach, in many families, the International Committee for the Taxonomy of Viruses taxonomy and can therefore be used as a proxy to viral species.

A recommendation of: Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sebastien Reynard, Kristian Stevens, Denis Kutnjak, Sebastien Massart Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection 10.5281/zenodo.4584718

International audience; A novel geminivirus was identified in France and Spain in asymptomatic plants of white clover (Trifolium repens) and shrub medick (Medicago arborea). Its genome has the hallmarks of a capulavirus, and its relationship to other capulaviruses was confirmed by phylogenetic analysis. White clover isolates formed a tight cluster in the phylogenetic tree, while shrub medick isolates formed two distinct, more divergent groups with sequence identity values close to the species cutoff. These three groups have likely participated in recombination events involving alfalfa leaf curl virus and French bean severe leaf curl virus. The name "trifolium virus 1" (TrV1) is proposed for this new Capulavirus. Three TrV1 genotypes (TrV1-A, TrV1-B, and TrV1-C) were clearly distinguished.

Supplementary Materials - Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

Huge efforts are currently underway to address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct regulatory and signaling networks. However, assembling networks implies manual operations due to source-specific identification of biological entities and relationships, multiple life-science databases with redundant information and the difficulty of recovering logical flows in biological pathways. We propose a framework based on Semantic Web technologies to automate the reconstruction of large-scale regulatory and signaling networks in the context of tumor cells modeling and drug screening. The proposed tool is pyBRAvo (python Biological netwoRk Assembly), and here we have applied it to a dataset of 910 gene expression measurements issued from liver cancer patients. The tool is publicly available at https://github.com/pyBRAvo/pyBRAvo.

The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics pipelines for virus detection are available, making the choice of a suitable one difficult. A robust benchmarking is needed for the unbiased comparison of the pipelines, but there is currently a lack of reference datasets that could be used for this purpose. We present 7 semi-artificial datasets composed of real RNA-seq datasets from virus-infected plants spiked with artificial virus reads. Each dataset addresses challenges that could prevent virus detection. We also present 3 real datasets showing a challenging virus composition as well as 8 completely artificial datasets to test haplotype reconstruction software. With these datasets that address several diagnostic challenges, we hope to encourage virologists, diagnosticians and bioinformaticians to evaluate and benchmark their pipeline(s).

International audience; Although chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not clear. Using classical approaches and high-throughput sequencing (HTS) techniques, we identified a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted, and sequenced on an Illumina NextSeq500 (2 × 150 nt or 2 × 75 nt). In each source, we identified a single contig of ≈7.2 kb that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5%, with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons showed that this virus is a novel species; we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak) as well in chestnut trees presenting typical ChMD symptoms in the field (100 and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut sequence read archive transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the United States as well as ChMV detection in C. dentata from the United States. Preliminary epidemiological studies performed in France and central eastern Italy showed that ChMV has a high incidence in some commercial orchards and low within-orchard genetic diversity.

We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed. Electronic supplementary material The online version of this article (10.1007/s00705-020-04817-x) contains supplementary material, which is available to authorized users.

Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annota-tion revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name “Grapevine polerovirus 1” is proposed.

To characterize their virome, double stranded RNAs extracted from scrapings of two Iranian grapevine varieties held in the Vassal-Montpellier Grapevine Biological Resources Center were analysed by high-throughput sequencing. In addition to several well-known grapevine viruses, divergent isolates of the newly described grapevine Kizil Sapak virus were identified in both accessions. Four complete genome sequences were determined, as well as two additional partial sequences (1,580 and 3,849 nucleotides long). These genomic sequences highlight the molecular diversity of this poorly known virus. In view of the absence of amplification of the GKSV isolates characterized here using the published primer pair, novel degenerate, polyvalent primers were designed, providing a more robust diagnosis.

Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at the family level but also by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. A large viral diversity dominated by novel dsRNA viruses was detected in all sites, while a large between-site variability limited the ability to draw a clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 versus 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow us to reason methodological choices in phytovirome studies and likely in other virome studies where RNA viruses are the focal taxa. IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them but also on the comparative performance-methodological approaches for their study. We used and compared two viral sequence enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA), for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing us to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is recommended because it consistently provided a more comprehensive description of the analyzed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) is a cell-surface glycoprotein highly expressed in several tumor types including non-small cell lung cancer (NSCLC), colorectal cancer (CRC) and gastric cancer (GC). SAR408701 is an antibody-drug conjugate (ADC) which consists of anti-CEACAM5 antibody conjugated to the maytansinoid DM4 cytotoxic agent, a highly potent tubulin inhibitor. SAR408701 was investigated in a First in Human trial (FIH) in patients with advanced solid tumors. During the early dose escalation phase, preliminary anti-tumor activity was observed with objective response reported in 3 patients with CRC and 1 patient with GC. In an interim analysis of an ongoing expansion cohort of patients with non-squamous NSCLC and with CEACAM5 expression in ≥ 50% of tumor cells, 25% overall response rate (ORR) (8/32 evaluable patients) and 37.5% (12 patients) stable disease were observed. In parallel to FIH trial, several preclinical studies were performed to support the clinical development of SAR408701 in NSCLC, CRC and GC. A single mouse trial (SMT) was carried out on a panel of 28 patent-derived xenografts (PDX) covering the top 3 indications. The SMT format employs a single mouse per PDX model and treatment arm and uses RECIST criteria as readout. Results showed an efficacy profile in the preclinical trial close to that obtained in clinic with an ORR of 10% in CRC, of 50% in lung cancers and of 37.5% in GC. The efficacy of SAR408701 is correlated with CEACAM5 expression in lung and gastric indications. To further assess the potential of SAR408701 in NSCLC, preclinical investigations have been done to determine if an ADC-DM4 could be beneficially combined with immune checkpoint inhibitors (ICIs). The capacity of DM4-treated tumor cells to immunize immune competent mice to the tumor was evaluated, indicating that DM4 can induce immunogenic cell death. This result supports the development of SAR408701 in combination with ICIs in NSCLC. The combination of SAR408701 with 4 different standard of care (SoC) therapies were tested in 2 CRC PDX models, one sensitive and one resistant to SAR408701 alone. Combinations of SAR408701 were evaluated with either FOLFOX regimen, FOLFIRI regimen, TAS-102 or cetuximab. All combinations resulted in significantly better antitumor activity than single agent arms in both resistant and sensitive PDXs without an increase in toxicity and showed a therapeutic synergy. These results suggest that SAR408701 can be advantageously combined with SoC in gastro-intestinal (GI) cancers. In summary, preclinical data show that SAR408701 displays a strong antitumor activity as a single agent in NSCLC and in combination with SOC in GI cancers, supporting further development in these indications. Furthermore, SAR408701 could be a potential good candidate to be combined with ICIs in NSCLC. Citation Format: Stephanie Decary, Olivier Lemaitre, Anne-Marie Lefebvre, Alexandra Ferrier, Marielle Chiron, Dmitri Wiederschain, Anne-Sophie Lacoste-Bourgeacq, Nathalie Le Bail, Sukhvinder Sidhu, Cecile Combeau, Mustapha Chadjaa, Celine Nicolazzi. Preclinical efficacy data for the anti-CEACAM5-DM4 ADC SAR408701 supports further development in lung and gastro-intestinal cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 561.

User repair can prolong product lifespan and support in turn the transformative Circular Economy agenda. Current research concerning user motivations and propensity to repair differs as to the extent at which users’ environmental concerns influence repair propensity. Because of this, the focus of this study is on potential individuals with pro-environmental inclination, as a mean to identify the factors supporting and hindering repair. To this end, an in-depth survey exploring factors influencing repair propensity for electrical and electronic goods was executed. Findings from 208 respondents affiliated with pro-environmental communities identify innovativeness and frugality traits as significant factors influencing repair propensity. Qualitative analysis has shown the significance of financial considerations in deciding to repair or replace, and how access to helping relationships alleviate most of the barriers to repair, including lack of access to repair shops and lack of knowledge and skills. The findings of this study provide much needed insight into repair behaviour. Furthermore, the insights provided will aid researchers and policy makers to develop appropriate interventions to support repair.

UMR BFP - Equipe Virologie; International audience; As part of a grapevine metagenome study, total RNA extracted from grapevine phloem scrapings was analyzed by Illumina sequencing. For one 420A rootstock sample, reads mapping against a reference database and BLAST annotation of contigs identified the presence of a divergent isolate of Botrytis virus F (BVF). The full genome sequence of this isolate (IVC-5-77) was determined (6,828 nucleotides [nt], excluding the poly(A) tail) and shown to be collinear with that of the BVF reference isolate, with the two open reading frames encoding a replication-associated protein (REP) and a coat protein (CP). The IVC-5-77 isolate, however, is very divergent, showing only 81.3-81.6% nucleotide sequence identity to the two other sequenced BVF isolates. The internal non-coding region was also found to be highly variable between BVF isolates. Analysis of the RNASeq reads demonstrated that close to 20% of them belong to Botrytis cinerea, the putative host of the IVC-5-77 isolate. These results extend our knowledge of the diversity and variability of BVF and demonstrate its detectability, together with that of its B. cinerea host, in total RNA RNASeq data from grapevine phloem scrapings.

Activation of the MET/HGF pathway is common in human cancer and is thought to promote tumor initiation, metastasis, angiogenesis, and resistance to diverse therapies. We report here the pharmacologic characterization of the triazolopyridazine derivative SAR125844, a potent and highly selective inhibitor of the MET receptor tyrosine kinase (RTK), for intravenous administration. SAR125844 displayed nanomolar activity against the wild-type kinase (IC50 value of 4.2 nmol/L) and the M1250T and Y1235D mutants. Broad biochemical profiling revealed that SAR125844 was highly selective for MET kinase. SAR125844 inhibits MET autophosphorylation in cell-based assays in the nanomolar range, and promotes low nanomolar proapoptotic and antiproliferative activities selectively in cell lines with MET gene amplification or pathway addiction. In two MET-amplified human gastric tumor xenograft models, SNU-5 and Hs 746T, intravenous treatment with SAR125844 leads to potent, dose- and time-dependent inhibition of the MET kinase and to significant impact on downstream PI3K/AKT and RAS/MAPK pathways. Long duration of MET kinase inhibition up to 7 days was achieved with a nanosuspension formulation of SAR125844. Daily or every-2-days intravenous treatment of SAR125844 promoted a dose-dependent tumor regression in MET-amplified human gastric cancer models at tolerated doses without treatment-related body weight loss. Our data demonstrated that SAR125844 is a potent and selective MET kinase inhibitor with a favorable preclinical toxicity profile, supporting its clinical development in patients with MET-amplified and MET pathway–addicted tumors. Mol Cancer Ther; 14(2); 384–94. ©2014 AACR.

The objective of this paper is to evaluate the importance of selected characteristics of innovation networks in affecting the decision of food SMEs when joining such networks. The paper develops and tests a series of hypotheses through a choice experiment exercise ran on a sample of 231 firms in six EU countries. The results showed that SMEs prefer networks that are composed of manufacturers and supply chain members, where information is shared confidentially among network partners, and when the network provides support to help the firm build its own networks of partners for innovation. In addition, SMEs' choice of the network is also affected by the interaction between specific network attributes and two firm characteristics, i.e. the firm's collaborative experience and innovation objectives. Based on the results, we conclude that the success of inter-organizational networks depends on the fit between the network's design and the innovation and networking behaviour of the firms.

The objective of this paper is to evaluate the importance of selected characteristics of innovation networks in affecting the decision of food SMEs when joining such networks. The paper develops and tests a series of hypotheses through a choice experiment exercise ran on a sample of 231 firms in six EU countries. The results showed that SMEs prefer networks that are composed of manufacturers and supply chain members, where information is shared confidentially among network partners, and when the network provides support to help the firm build its own networks of partners for innovation. In addition, SMEs' choice of the network is also affected by the interaction between specific network attributes and two firm characteristics, i.e. the firm's collaborative experience and innovation objectives. Based on the results, we conclude that the success of inter-organizational networks depends on the fit between the network's design and the innovation and networking behaviour of the firms.

Dix ans se sont écoulés depuis le jugement Montfort, qui consacrait l’Hôpital comme une composante essentielle de la vitalité des communautés francophones en situation minoritaire. Jusqu’à quel point cette reconnaissance du droit à un service en français, accessible dans des établissements localisés dans les milieux dans lesquels la minorité évolue, a-t-elle mené à une ambition plus territoriale chez les intervenants francophones ? L’analyse des propos tenus par 38 participants à un exercice de cartographie conceptuelle sur l’avenir des services de santé en français en Ontario révèle qu’ils ne s’aventurent pas très loin sur le terrain des modalités de l’édification d’un véritable territoire francophone en santé. L’institution est évoquée, mais davantage comme un projet appartenant à un horizon lointain que comme un enjeu actuel. En guise de conclusion, les auteures se sont interrogées sur les effets d’une telle vision sur l’avenir des services de santé en français., Ten years ago the ruling on the Montfort Hospital in Ottawa recognized health as an essential component of the life of francophone minorities. To what extent has the right to be served in French in local health institutions lead to territorial aspirations within the francophone leadership? This paper analyses the interventions by 38 participants in a virtual cartography exercise on the future of health services offered to Franco-Ontarians. As far as health is concerned, the results show that participants were reluctant to construct a distinct francophone territory. Institutions were mentioned but seen only as a distant goal rather than a current concern. The impact of such a response on the future of health services in French is explored.

Summary Objective The purpose of this randomized multicentric study was to evaluate the diagnostic contribution of screening for HCV infection on saliva samples in day-to-day practice in the intraveneous drug-user (IVDU) population. Methods Between January and May 2004, 274 presumably HCV-negative IVDU were screened for HCV infection in 15 centers in France (median age 29 years). After centralized randomization, screening tests were performed on blood samples (arm A) or saliva samples (arm B). Screening tests were performed in 78 subjects (28%) had never been screened before and in 196 subjects (72%) who had had a negative HCV screening test on average 12 months prior to the beginning of the study. In the event of a positive saliva test for anti-HCV Ab, a serum test for anti-HCV Ab was performed. In the event of a positive serum test for anti-HCV Ab, PCR was performed on serum to measure HCV-RNA. Results Fourteen individuals were positive for HCV RNA (7 in each arm). Six of these cases had not been detected before. In eight cases, the median time between the last negative screening test and study inclusion was 11 months (range 6-94 months). Conclusions Viremia tests were positive in 5% percent of the target population, although one-third of the individuals in arm A (blood samples) were not tested. The saliva test may be a useful alternative in the event of refusal of a blood test or when poor venous conditions compromise venous puncture. A confirmatory blood test still remains difficult to obtain in nearly half of patients.

Au cours des vingt dernieres annees, le plaidoyer est devenu une pratique courante et institutionnalisee, mise en œuvre par les associations et organisations internationales dans leurs strategies de mobilisation. Malgre tout, il n’existe encore aucune definition consensuelle qui regrouperait la multiplicite de pratiques reconnues derriere ce terme. Deux elements peuvent ressortir des pratiques de plaidoyer : une volonte de « faire faire », autrement dit une visee d’influence et de mobilisatio...

For several years now, the CNIB has been working diligently on finding innovative solutions to provide to the blind and vision-impaired community better access to literary materials and information through the application of new information technology. Efforts have culminated in the development of a digital library with accessible on-line services. An important project funded by the Office of Learning Technology (OLT) of Human Resources and Development Canada was undertaken in order to gather information data about literacy and training needs of blind and vision impaired persons. Phase one has been completed and consisted in conducting a survey among 500 registered CNIB Quebec library clients and creating a community learning network regrouping partners. The creation of a community learning network has allowed the CNIB to unite partners of different fields, such as education, rehabilitation, technology, community centers and organizations that specialize in the provision of information services. Part of the CNIB's efforts must now be directed on helping blind and vision-impaired persons maximize the use of this new technology.

The nuclear receptor PPARgamma is implicated in the control of cell proliferation and apoptosis. However, the molecular mechanisms by which it controls these processes remain largely elusive. We show here that PPARgamma activation in the presence of the retinoblastoma protein (RB) results in the arrest of cells at the G1 phase of the cell cycle, whereas in the absence of RB, cells accumulate in G2/M, endoreduplicate, and undergo apoptosis. Through the use of HDAC inhibitors and coimmunoprecipitations, we furthermore demonstrate that the effects of RB on PPARgamma-mediated control of the cell cycle and apoptosis depend on the recruitment of histone deacetylase 3 (HDAC3) to PPARgamma. In combination, these data hence demonstrate that the effects of PPARgamma on cell proliferation and apoptosis are dependent on the presence of an RB-HDAC3 complex.

Resume – Chez le medecin balzacien, en suivant six heros medecins de La Comedie humaine, le lecteur decouvre l’interieur d’un bourgeois le plus souvent aise, voire riche, et marque beaucoup plus par son appartenance sociale que par sa profession : on y voit de beaux meubles et objets mais tres peu d’instruments medicaux, et seulement lorsqu’ils sont indispensables au recit. En outre, Balzac semble s’inspirer des prejuges vehicules par la satire du temps, notamment dans Les Francais peints par eux-memes, par l’article Le Medecin par Louis Roux, paru en 1840 chez Curmer ; son realisme est, au moins en ce domaine, plus litteraire que pris sur le vif.

Background: Identification of MET genetic alteration, mutation, or amplification in oropharyngeal squamous cell carcinoma (OPSCC) could lead to development of MET selective kinase inhibitors. The aim of this study was to assess the frequency and prognostic value of MET gene mutation, amplification, and protein expression in primary OPSCC.Methods: A retrospective chart review was conducted of patients treated for single primary OPSCC between January 2007 and December 2009. Pre-treatment OPSCC tissue samples were analyzed for MET mutations, gene amplification, and overexpression using Sanger sequencing, FISH analysis, and immunohistochemistry respectively. Univariate and multivariate analyses were used to analyze correlations between molecular abnormalities and patient survival.Results: 143 patients were included in this study. Six cases (4%) were identified that had a genetic variation, but previously described mutations such as p. Tyr1235Asp (Y1235D) or p.Tyr1230Cys (Y1230C) were not detected. There were 15 high polysomy cases, and only 3 cases met the criteria for true MET amplification, with >= 10% amplified cells per case. Immunohistochemistry evaluation showed 43% of cases were c-MET negative and in 57% c-MET was observed at the tumor cell level. Multivariate analysis showed no significant association between MET mutation, amplification, or expression and survival.Conclusions: Our study shows a low frequency of MET mutations and amplification in this cohort of OPSCC. There was no significant correlation between MET mutations, amplification, or expression and patient survival. These results suggest that patient selection based on these MET genetic abnormalities may not be a reliable strategy for therapeutic intervention in OPSCC.

Our recent studies have demonstrated that PPARalpha activators stimulate differentiation and inhibit proliferation in cultured human keratinocytes and accelerate epidermal development and permeability barrier formation in fetal rat skin explants. As the role of PPARalpha activation in adult epidermis is not known, the aim of this study was to determine if topically applied PPARalpha ligands regulate keratinocyte differentiation in murine epidermis. Topical treatment with PPARalpha activators resulted in decreased epidermal thickness. Expression of structural proteins of the upper spinous/granular layers (involucrin, profilaggrin-filaggrin, loricrin) increased following topical treatment with PPARalpha activators. Furthermore, topically applied PPARalpha activators also increased apoptosis, decreased cell proliferation, and accelerated recovery of barrier function following acute barrier abrogation. Experiments with PPARalpha-/- knockout mice showed that these effects are specifically mediated via PPARalpha. Compared with the epidermis of PPARalpha+/+ mice, involucrin, profilaggrin-filaggrin, and loricrin expression were slightly decreased in PPARalpha-/- mice. Moreover, topical clofibrate treatment did not increase epidermal differentiation in PPARalpha-/- mice. Furthermore, in cultured human keratinocytes we have demonstrated that PPARalpha activators induce an increase in involucrin mRNA levels. We have also shown that this increase in gene expression requires an intact AP-1 response element at -2117 to -2111 bp. Thus, stimulation of PPARalpha stimulates keratinocyte/epidermal differentiation and inhibits proliferation.

Lipidated angiotensin II (Ang) agonists and antagonists were synthesized and evaluated for their biological activities for eventual use an antimyoproliferative agents. Solid phase peptide synthesis was used for the assembly of the peptides with the Fmoc protection scheme. N-Acetyl-Ser1 Ang was palmitoylated on the serine hydroxyl function. The nonpalmitoylated analogue retained one-third of Ang's affinity toward the AT1 receptor on bovine adrenal cortex membranes, and the palmitoylated analogue was essentially inactive. Upon enzymatic lipolysis or mild saponification of the palmitoylated peptide, biological activity was restored. An analogous compound of Ang, N-acetyl-Ser1,beta-D-naphthylalanine8 ([NAcSer1,D-Nal8]Ang), was a pure antagonist on rabbit aorta but with lower affinity. Its O-palmitoylated form was inactive as well but was easily converted to the nonlipidated active form by lipolysis or saponification. Direct palmitoylation of [sarcosine1]Ang with palmitoyl chloride was obtained on the free phenolic hydroxyl of Tyr4 on solid phase on an otherwise fully protected peptide. This lipopeptide was fully active, was comparable to [Sar1]Ang, and exhibited strongly prolonged activity. Lipolysis and saponification under mild conditions yielded standard [Sar1]Ang. The corresponding [Sar1,D-Nal8]Ang was a potent and very long-lasting antagonist (pA2 = 8.1), and its analogous palmitoyl phenyl ester in position 4 was active in its palmitoylated form (antagonist) and, again, returned to the nonlipidated form upon saponification or lipolysis. [Sar1,Tyr4(O-octadecyl)]Ang, an analogue to Tyr-palmitoylated [Sar1]Ang with an octadecyl phenyl ether in position 4, was also prepared. Surprisingly, the ether compound was inactive. Premature hydrolysis of the palmitoyl phenyl ester peptide was excluded by HPLC analysis, and the activity of the ester peptide is attributed to a putative hydrogen bond that may be critical for biological activity. The discovery of potent biologically active lipidated antagonists of Ang gives access to potential antimyoproliferative agents with numerous application possibilities.