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Objective: To determine whether human pre-implantation embryos have the potential to be infected by SARS-CoV-2, the virus responsible for COVID-19 Design: Assessment of expression levels of SARS-CoV-2 entry mediators in human embryo biopsies by RNAseq analysis, and infection of cultured embryos with SARS-CoV-2 Spike glycoprotein pseudotyped reporter virions expressing green fluorescent protein (GFP) Materials and Methods: Trophectoderm biopsies from blastocyst-stage embryos (n=24) were processed for RNAseq using a commercial kit and sequenced;results were analyzed for expression of factors implicated in SARS-CoV-2 cellular entry For viral infection experiments, blastocyst-stage embryos (n=94) were hatched from zonas mechanically, and infected by spinoculation with GFP-reporter virions pseudotyped with the SARS-CoV-2 Spike glycoprotein (required for SARS-CoV-2 entry) Embryos were subsequently monitored for fluorescence at 24-48 hours post-infection Various control conditions were used as specified in the ‘results’ section A mixed population of euploid, aneuploid, and untested embryos used in the study were from IVF treatment, donated to research by signed informed consent The project was approved by an Institutional Review Board Results: Cells collected from blastocyst-stage embryos robustly expressed the canonical SARS-CoV-2 entry receptor ACE2 and the putative activator protease TMPRSS2, in addition to other reported entry factors Embryos exposed to reporter virions pseudotyped with SARS-CoV-2 Spike glycoprotein displayed robust GFP signal, often in numerous cells with cytoplasmic localization Specificity was confirmed by the absences of fluorescence in embryos treated with virions lacking the Spike glycoprotein (“bald” virus), or when embryos were spinoculated with media alone in the absence of virus Embryos exposed to Spike glycoprotein-positive reporter virus in the presence of neutralizing anti Spike- or anti-ACE2-blocking antibodies exhibited negligible GFP signal, while control monoclonal IgG antibody-treated embryos maintained GFP expression These results implicated the canonical Spike-ACE2 axis in the viral entry Lastly, embryos exposed to reporter virions pseudotyped with Spike glycoprotein of SARS-CoV-1 (which also enters cells via ACE2) displayed GFP fluorescence, while embryos exposed to reporter viruses pseudotyped with Spike glycoprotein of MERS (which utilizes Dipeptidyl Peptidase IV (DPP4) instead of ACE2) resulted in no fluorescence Conclusions: Our results indicate that cells present in pre-implantation embryos are permissive to the canonical Spike-ACE2 viral entry mechanism utilized by SARS-CoV-2 These results encourage further investigation into the potential of SARS-CoV-2 infection in human embryos and may have wider implications in natural conception and ART practice

Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3’ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.

Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3′ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.

Maize leaves have distinct tissues that serve specific purposes. The blade tilts back to photosynthesize and the sheath wraps around the stem to provide structural support and protect young leaves. At the junction between blade and sheath are the ligule and auricles, both of which are absent in the recessive liguleless1 (lg1) mutant. Using an antibody against LG1, we reveal LG1 accumulation at the site of ligule formation and in the axil of developing tassel branches. The dominant mutant Wavy auricle in blade1 (Wab1-R) produces ectopic auricle tissue in the blade and increases the domain of LG1 accumulation. We determined that wab1 encodes a TCP transcription factor by positional cloning and revertant analysis. Tassel branches are few and upright in the wab1 revertant tassel and have an increased branch angle in the dominant mutant. wab1 mRNA is expressed at the base of branches in the inflorescence and is necessary for LG1 expression. wab1 is not expressed in leaves, except in the dominant mutant. The domain of wab1 expression in the Wab1-R leaf closely mirrors the accumulation of LG1. Although wab1 is not needed to induce lg1 expression in the leaf, LG1 is needed to counteract the severe phenotype of the dominant Wab1-R mutant. The regulatory interaction of LG1 and WAB1 reveals a link between leaf shape and tassel architecture, and suggests the ligule is a boundary similar to that at the base of lateral organs.

The knotted1 (kn1) homeobox (knox) gene family was first identified through gain-of-function dominant mutants in maize (Zea mays). Class I knox members are expressed in meristems but excluded from leaves. In maize, a loss-of-function phenotype has only been characterized for kn1. To assess the function of another knox member, we characterized a loss-of-function mutation of rough sheath1 (rs1). rs1-mum1 has no phenotype alone but exacerbates several aspects of the kn1 phenotype. In permissive backgrounds in which kn1 mutants grow to maturity, loss of a single copy of rs1 enhances the tassel branch reduction phenotype, while loss of both copies results in limited shoots. In less introgressed lines, double mutants can grow to maturity but are shorter. Using a KNOX antibody, we demonstrate that RS1 binds in vivo to some of the KN1 target genes, which could partially explain why KN1 binds many genes but modulates few. Our results demonstrate an unequal redundancy between knox genes, with a role for rs1 only revealed in the complete absence of kn1.

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc.

Next-generation sequencing is empowering a deeper understanding of biology by enabling RNA expression analysis over the entire transcriptome with high sensitivity and a wide dynamic range. One powerful application within this field is stranded RNA sequencing (RNA-seq), which is necessary to distinguish overlapping genes and to conduct comprehensive annotation and quantification of long non-coding RNAs. Commonly used methods for generating strand-specific RNA-seq libraries are often complicated by protocols that require several rounds of enzymatic treatments and clean-up steps, making them time-intensive, insensitive, and unsuitable for processing several samples simultaneously. An additional challenge in the generation of RNA-seq libraries from total RNA involves the high amount of ribosomal RNA (rRNA) in the starting material. This unit presents streamlined workflows for generating strand-specific RNA-seq libraries from 10 ng to 1 µg total RNA, representing a minimum of 1000 cells, in less than 7 hr with minimal carryover rRNA. These methods allow scientists to evaluate the expression of all transcripts, including non-polyadenylated long non-coding RNAs, even in limited biological samples. Combination of the RNase H-based RiboGone rRNA removal system and SMARTer Stranded RNA-seq technology enables depletion of over 95% of rRNA from mammalian samples, and direct production of Illumina-ready libraries that maintain strand-of-origin information. An alternate method for low input of highly degraded samples is also presented. © 2016 by John Wiley & Sons, Inc.

Leaf development presents a tremendous resource for tackling the question of patterning in biology. Leaves can be simple or highly dissected. They may have elaborated parts such as the tendrils of a pea leaf or the rolled blade of a carnivorous pitcher plant. Despite the variation in size, shape, and function, all leaves initiate in the same manner: from the flanks of a meristem. The maize leaf is useful for analysis of patterning due to the wealth of mutants and the distinct tissues along the proximal distal axis. The blade is distal, the sheath is proximal, and the ligule forms at the blade/sheath boundary. Establishment of this boundary involves the transcription factors LIGULELESS1 and LIGULELESS2 and the kinase LIGULELESS NARROW. The meristem-specific protein KNOTTED1 (KN1) binds and modulates the lg2 gene. Given the localization of KN1 at the proximal end of the leaf from the time of inception, we hypothesize that KN1 has a role in establishing the very proximal end of the leaf, whereas an auxin maximum guides the growing distal tip.

Maize (Zea mays) leaves provide a useful system to study how proximal/distal patterning is established because of the distinct tissues found in the distal blade and the proximal sheath. Several mutants disrupt this pattern, including the dominant knotted1-like homeobox (knox) mutants. knox genes encode homeodomain proteins of the TALE superclass of transcription factors. Class I knox genes are expressed in the meristem and down-regulated as leaves initiate. Gain-of-function phenotypes result from misexpression in leaves. We identified a new dominant allele of maize knotted1, Kn1-DL, which contains a transposon insertion in the promoter in addition to a tandem duplication of the kn1 locus. In situ hybridization shows that kn1 is misexpressed in two different parts of the blade that correlate with the different phenotypes observed. When kn1 is misexpressed along the margins, flaps of sheath-like tissue form along the margins. Expression in the distal tip leads to premature termination of the midrib into a knot and leaf bifurcation. The gain-of-function phenotypes suggest that kn1 establishes proximal/distal patterning when expressed in distal locations and lead to the hypothesis that kn1 normally participates in the establishment of proximal/distal polarity in the incipient leaf.

KNOTTED1 (KN1)-like homeobox (KNOX) transcription factors are involved in the establishment and maintenance of plant meristems; however, few direct targets of KNOX proteins have been recognized. Using a combination of double mutant analysis and biochemistry, we found that in maize (Zea mays), KN1 negatively modulates the accumulation of gibberellin (GA) through the control of ga2ox1, which codes for an enzyme that inactivates GA. The ga2ox1 mRNA level is elevated in immature leaves of dominant KNOX mutants and downregulated in reproductive meristems of the null allele kn1-e1. KN1 binds in vivo to an intron of ga2ox1 through a cis-regulatory element containing two TGAC motifs. VP16-KN1 activates transcription in planta from a chimeric promoter containing this binding site. The domains of expression of kn1 and ga2ox1 mRNAs overlap at the base of the shoot apical meristem and the base of newly initiated leaves, suggesting that KN1-mediated activation of ga2ox1 maintains a boundary between meristem cell identity and rapidly elongating cells of the shoot. The KN1 binding site is conserved in ga2ox1 genes of different grasses, suggesting that the local regulation of bioactive GA levels through KNOX proteins is a common theme in grasses.

French Abstract: L’avenement des nouvelles technologies dans le milieu de la sante est souvent accueilli avec un certain scepticisme par la communaute medicale et ethico-juridique. En effet, la validite analytique et l’utilite clinique de ces outils ainsi que les consequences de leur utilisation sur l’analyse des responsabilites des medecins et autres professionnels de la sante demeurent sujets de debats. Une chose est claire : le medecin dans cette nouvelle ere fera face a plusieurs defis. Ceci dit, les nouvelles technologies ouvriront egalement la porte a plusieurs opportunites. Afin de discuter de ces points plus en profondeur, le Centre de genomique et politiques de l’Universite McGill a invite, le 30 mai dernier, des medecins, des juristes, des ethiciens, des conseillers en genetique ainsi que des membres des comites d’ethique a venir participer a un atelier intitule : « Le medecin face aux nouvelles technologies dans le domaine medical : nouvelles responsabilites? ». L’atelier avait deux objectifs precis : 1) familiariser les participants avec les obligations juridiques du medecin; 2) identifier et debattre des consequences de l’utilisation des nouvelles technologies sur les obligations juridiques du medecin. Trois cas pratiques composes de quatre grandes questions ont ete presentes aux participants. Chaque cas a couvert un domaine specifique, soit 1) le sequencage du genome entier; 2) les tests genetiques offerts directement aux consommateurs; et 3) les outils de detection rapide d’infections. Bien que l’accent ait ete mis sur le role du medecin, les questions ont eu pour but d’aborder egalement le role des divers acteurs dans le milieu de la recherche et de la pratique clinique. Ce rapport final exposera les resultats de ces echanges et les reponses des intervenants aux questions soumises. English Abstract: The advent of new technologies in the healthcare environment is often welcomed with some skepticism by the medical and ethical-legal community. The analytical validity and clinical utility of these tools, as well as the consequences of their use on the analysis of the responsibilities of physicians and other health professionals, remain debatable. One thing is clear: the physician in this new era will face several challenges. This being said, new technologies will also open the door to several opportunities. To address these issues in greater depth, the McGill Center of Genomics and Policy invited, on May 30th 2012, physicians, lawyers, ethicists, genetic counselors, and members of ethics committees, to attend a workshop entitled "The physician facing new technologies in the medical field: new responsibilities? ". The workshop had two specific objectives: 1) familiarize participants with the physician's legal obligations; 2) identify and discuss the consequences of the use of new technologies on the physician's legal obligations. Three practical cases with four main questions were presented to participants. Each case covered a specific domain, ie 1) whole-genome sequencing; (2) direct-to-consumer genetic tests; And 3) tools for rapid detection of infections. Although the emphasis was on the role of the physician, the questions were also intended to address the role of the various stakeholders in the research and clinical practice setting. This final report will present the results of these exchanges and the answers of the speakers to the questions submitted.

 Premise of the study: How a leaf acquires its shape is a major and largely unresolved question in plant biology. This problem is particularly complex in the case of compound leaves, where the leaf blade is subdivided into leafl ets. In many eudicots with compound leaves, class I KNOTTED1-LIKE HOMEOBOX ( KNOX ) genes are upregulated in the leaf primordium and promote leafl et initiation, while KNOX genes are restricted to the shoot apical meristem in simple-leaved plants. In monocots, however, little is known about the extent of KNOX contribution to compound leaf development, and we aimed to address this issue in the palm Chamaedorea elegans .  Methods: We investigated the accumulation pattern of KNOX proteins in shoot apical meristems and leaf primordia of the palm C. elegans using immunolocalization experiments.  Key results: KNOX proteins accumulated in vegetative and infl orescence apical meristems and in the subtending stem tissue, but not in the plicated regions of the leaf primordia. These plicated areas form during primary morphogenesis and are the only meristematic tissue in the developing primordium. In addition, KNOX proteins did not accumulate in any region of the developing leaf during secondary morphogenesis, when leafl ets separate to create the fi nal pinnately compound leaf.  Conclusions: The compound leaf character in palms, C. elegans in particular and likely other pinnately compound palms, does not depend on the activities of KNOX proteins.

Protein coding genes constitute approxi- mately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., ''whole exome'') have the potential to contribute our understanding of human diseases. We used a method for whole-exome sequencing coupling Agilent whole-exome capture to the Illumina DNA-sequencing platform, and investigated two unre- lated fetuses from nonconsanguineous families with Fowler Syndrome (FS), a stereotyped phenotype lethal disease. We report novel germline mutations in feline leukemia virus subgroup C cellular-receptor-family member 2, FLVCR2, which has recently been shown to cause FS. Using this technology, we identified three types of genetic abnormalities: point-mutations, insertions- deletions, and intronic splice-site changes (first patho- genic report using this technology), in the fetuses who both were compound heterozygotes for the disease. Although revealing a high level of allelic heterogeneity and mutational spectrum in FS, this study further illustrates the successful application of whole-exome sequencing to uncover genetic defects in rare Mendelian disorders. Of importance, we show that we can identify genes underlying rare, monogenic and recessive diseases using a limited number of patients (n 52), in the absence of shared genetic heritage and in the presence of allelic heterogeneity.

Homeodomain proteins are well-characterized developmental regulators that control expression of target genes through sequence-specific DNA binding. The homeodomain forms a trihelical structure, with the third helix conferring specific interactions with the DNA major groove. A specific class of plant homeodomain proteins, called KNOX [KNOTTED1 (KN1)-like homeobox], also has the ability to signal between cells by directly trafficking through intercellular channels called plasmodesmata. Trafficking is mediated by a signal that is also contained within the homeodomain. Movement protein binding protein 2C was identified as a protein that interacts with the KN1 homeodomain and regulates the cell-to-cell trafficking of KN1 by sequestering the protein on microtubules. Therefore, KN1 has multiple potential cellular addresses, each of which is conferred by its homeodomain.

The protein Bax Inhibitor-1 (BI-1) has recently emerged as a negative regulator of plant programmed cell death (PCD), but how it functions at the biochemical level remains unknown. To elucidate its regulation and mode of action, we used suspension cells of Nicotiana tabacum to study the effects of cytokinins (CKs) on the expression level of NtBI-1 via western analysis. We found that the NtBI-1 protein is up-regulated following treatments with CKs at concentrations inducing a stress response (determined by growth reduction and PR1a accumulation), but not at PCD-inducing concentrations. These data point toward a role for NtBI-1 in the stress response to CKs. Application of CKs was also accompanied by a rapid cytosolic Ca(2+) pulse, and inhibition of this pulse with La(3+) or EGTA partially restored viability, indicating a signaling role for Ca(2+) in CK-induced cell death. However, CK-induced NtBI-1 accumulation was not altered by pretreatment with La(3+), nor by treatment with several modulators of intracellular Ca(2+) homeostasis and signaling, suggesting that CK-dependent regulation of NtBI-1 accumulation is not directly mediated by Ca(2+).

We have cloned the Candida albicans TPK2 gene encoding a cAMP-dependent protein kinase (PKA) catalytic subunit and generated a tpk2 homozygous null mutant to assess its ability to germinate in liquid media. N-acetylglucosamine (GlcNAc)-induced germ-tube formation was attenuated in the tpk2 strain and enhanced by compounds that are known to increase the PKA activity in situ. Germination was completely blocked in the presence of the myristoylated derivative of the heat-stable PKA inhibitor (MyrPKI). These results indicate that TPK1 acts positively in regulating the morphogenetic transition in C. albicans in the absence of the TPK2 gene. We were able to identify an mRNA from this second form of PKA in both wild-type and tpk2 null mutant cells. We found that PKA activity measured in the mutant lacking the TPK2 gene was about 10% of that displayed by the wild-type. The finding that the germinative response of tpk2 null mutant to serum was severely diminished at low serum concentrations indicates that the level of PKA is an important determinant of filamentous growth at low serum concentrations. The extent of germination attained at higher serum concentrations (5%) was similar in the wild-type and in the tpk2 null mutant strains suggesting that under these conditions germination was triggered through a PKA-independent pathway. Fil: Cloutier, Monikca. GREB Laval University; Canadá Fil: Castilla Lozano, Maria del Rocio. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Invetigaciones Bioquímicas y Fisiologicas; Argentina Fil: Bolduc, Nathalie. GREB Laval University; Canadá Fil: Zelada, Alicia Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Invetigaciones Bioquímicas y Fisiologicas; Argentina Fil: Martineau, Philippe. GREB Laval University; Canadá Fil: Bouillon, Marlène. GREB Laval University; Canadá Fil: Magee, Beatrice B.. University of Minnesota; Estados Unidos Fil: Di Bernardo, Maria Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Invetigaciones Bioquímicas y Fisiologicas; Argentina Fil: Giasson, Luc. GREB Laval University; Canadá Fil: Cantore, Maria Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Invetigaciones Bioquímicas y Fisiologicas; Argentina

Bax inhibitor-1 (BI-1) protein is proposed to be a conserved programmed cell death suppressor. In this report, we investigate the anti-apoptotic function of plant BI-1 by antisense (AS) down regulation of NtBI-1 in Nicotiana tabacum cv. BY-2 cells. We observed that AS cell lines were more susceptible to autophagy, internucleosomal DNA fragmentation and death than control cells when subjected to sucrose starvation and hypo-osmotic shock, in agreement with a role of BI-1 as a death inhibitor.

To date, few homologues of animal programmed cell death (PCD) regulators have been identified in plants. Among these is the plant Bax Inhibitor-1 (BI-1) protein, which possesses, like its human counterpart, the ability to suppress Bax-induced lethality in yeast cells. As the role of BI-1 in the regulation of plant PCD remains to be elucidated, we cloned BnBI-1 and NtBI-1 from cDNA libraries of oilseed rape ( Brassica napus L.) and tobacco ( Nicotiana tabacum L.). The analysis of the deduced amino acid sequences of BnBI-1 and NtBI-1 indicated that these proteins share a relatively high level of identity with other plant BI-1 proteins (73-95%) as well as with animal BI-1 proteins (26-42%). Comparative analysis with other available plant BI-1 proteins allowed the establishment of a structural model presenting seven transmembrane domains. Moreover, transient co-transfection of Bax with BnBI-1 or NtBI-1 in human embryonic kidney 293 cells revealed that both proteins can substantially inhibit apoptosis induced by Bax overexpression. Localization studies were also conducted using stable transformation of tobacco BY-2 cells and Saccharomyces cerevisiae, or transient expression in tobacco leaves, with the fusion protein BnBI-1GFP under control of the cauliflower mosaic virus 35S promoter. All transformants showed a fluorescence pattern of distribution typical of an endoplasmic reticulum (ER) protein. Results from differential permeabilization experiments in BY-2 cells expressing BnBI-1GFP also showed that the C-terminus is located on the cytosolic side of the ER. Taken altogether, our results suggest that BI-1 is evolutionarily conserved and could act as a key regulator of a death pathway common to plants and animals.

Coalition theory has developed outside the field of international relations in the wake of game theory, in laboratory experiments, and in the study of government coalitions. Four parameters can be used to predict the formation and development of coalitions : the benefits sought by the players, the resources at their disposal, the non-utilitarian linkages between them, and the decision threshold to be reached. In the field of international relations, many studies have dealt with coalitions, alignments, and interstate alliances. They can be grouped into three schools of thought. First, there is the economic school where States are seen as seeking to maximize the benefits they gain from working together. Second, there is the power relationship school, with States forging alliances mainly for self-protection from external military threats. Finally, there is the structural school, less developed than the two other ones, which is based on the affinities, rivalries, or neutralities between States. The effects of alliances, in particular military ones, have been much debated. Some authors claim they are a factor for stability in the international System ; others claim the opposite. The research note concludes by suggesting there is a need to develop a truly political theory of alliances, one that could integrate theories more economic or sociological in nature.

Au printemps 2001, la lutte contre la pauvreté et l’exclusion sociale figure au titre des défis majeurs du Québec dans la poursuite de son développement social et économique. Le Discours sur le budget en fait foi : 815 millions de dollars sont alors consentis sur trois ans à cette lutte, dont 100 millions en vue d’investissements structurants devant favoriser l’émergence de nouvelles initiatives de solidarité sociale. Dans cette foulée, une somme de 10 millions était octroyée pour la mise en oeuvre de projets de sécurité alimentaire visant à améliorer l’autonomie des familles. Les auteures voient dans cette mesure, même modeste, une ouverture significative à l’égard de la sécurité alimentaire. Qui plus est, ce thème s’inscrit en 2002 dans la loi visant à lutter contre la pauvreté et l’exclusion sociale. Les auteures proposent comme explication à cette ouverture un « effet de contagion » qui a pu se réaliser pleinement par l’action convergente de trois courants – celui des problèmes, celui des solutions et celui de la politique – et des acteurs qui y ont pris part., In the spring 2001, the fight against poverty and social exclusion appears one of the major priorities of the Government of Québec in the pursuit of its social and economic development. 815 M$ over a three-year period were thus allocated for this fight, including a 100 M$ social solidarity reserve to fund formative investments geared toward new initiatives of social solidarity. Among these investments, 10 M$ were allocated for the implementation of food security projects aimed at enhancing family food autonomy. Despite the modesty of this investment, the authors see in this announcement a significant opening toward food security. Moreover, in 2002, food security becomes entrenched in an act to combat poverty and social exclusion. As an explanation to this opening, this article proposes a "spillover" effect that had been fully realised by the coupling of three streams, that of problems, solutions, and politics, and the influence of policy entrepreneurs.

Background ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo “library preparation” to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. Results In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a “gold standard” reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. Conclusions We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3135-y) contains supplementary material, which is available to authorized users.