Targeting individual cells by barcode in pooled sequence libraries

Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.National Institute of Allergy and Infectious Diseases (U.S.) (U24AI11866803)National Human Genome Research Institute (U.S.) (RM1HG00619307)Broad Institute of MIT and HarvardBurroughs Wellcome Fund (Career Award at the Scientific Interface)National Science Foundation (U.S.). Graduate Research FellowshipNational Human Genome Research Institute (U.S.). Centers of Excellence in Genomic Science (RM1HG00619307)Massachusetts Institute of Technolog

Discourir pour présider

Peut-on être acteur politique sans parler de façon efficace ? Le film de Tom Hooper, Le Discours d’un roi (2010), suffirait à nous convaincre du contraire. Il a fallu à George VI surmonter son bégaiement pour assumer pleinement son rôle lorsqu’il s’est agi de mobiliser son peuple pour la guerre qui s’annonçait, en septembre 1939. A fortiori, lorsque les règles d’accès au pouvoir sont de nature démocratique, l’exigence semble devenir totalement incontournable. En France comme dans de nombreux ..

Early Illustrations of Geste Antagoniste in Cervical and Generalized Dystonia

Background: Geste antagoniste, or sensory trick, is a voluntary maneuver that temporarily reduces the severity of dystonic postures or movements. We present a historical review of early reports and illustrations of geste antagoniste. Results: In 1894, Brissaud described this phenomenon in Paris in patients with torticollis. He noted that a violent muscular contraction could be reversed by a minor voluntary action. He considered the improvement obtained by what he called “simple mannerisms, childish behaviour or fake pathological movements” was proof of the psychogenic origin of what he named mental torticollis. This concept was supported by photographical illustrations of the patients. The term geste antagoniste was used by Brissaud’s pupils, Meige and Feindel, in their 1902 monograph on movement disorders. Other reports and illustrations of this sign were published in Europe between 1894 and 1906. Although not mentioned explicitly, geste antagoniste was also illustrated in a case report of generalized dystonia in Oppenheim’s 1911 seminal description of dystonia musculorum deformans in Berlin. Discussion: Brissaud-Meige’s misinterpretation of the geste antagoniste unfortunately anchored the psychogenic origin of dystonia for decades. In New York, Herz brought dystonia back into the realm of organic neurology in 1944. Thereafter, it was given prominence by other authors, notably Fahn and Marsden in the 1970–1980s. Nowadays, neurologists routinely investigate for geste antagoniste when a dystonic syndrome is suspected, because it provides a further argument in favor of dystonia. The term alleviating maneuver was proposed in 2014 to replace sensory trick or geste antagoniste. This major sign is now part of the motor phenomenology of the 2013 Movement Disorder Society’s classification of dystonia

Near ambient pressure X-ray photoelectron spectroscopy monitoring of the surface immobilization cascade on a porous silicon-gold nanoparticle FET biosensor

Porous silicon (PSi) offers extremely attractive optical, electronic and biofunctional properties for the development of biosensors. In the present work, we have studied the step by step sandwich biofunctionalization cascade of a PSi platform by near ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) and, in parallel, we have developed a three electrode PSi device sensitive to changes in surface conductance. Prior to the NAP-XPS characterization, the organosilanization with glycidyloxy-propyl-trimethoxy-silane, the bioconjugation, and the gold nanoparticle (AuNP) sensitization layer were monitored by spectroscopic ellipsometry. The NAP-XPS analysis revealed outstanding results: a) the NAP-XPS chamber allows detecting the pristine PSi with negligible adventitious carbon contamination, b) the single oxygen bonded carbon component of the Glycidyl group dominates the C1s core level after organosilanization, c) the good progress of the biofunctionalization/recognition is confirmed by the increase of the silica to silicon component ratio in the Si2p core level and, d) the N1s core level describes identical features from the presence of aminoacid sequences in the capture/detection steps. A FET sensing of a prostate specific antigen (PSA) marker was performed through conjugation with AuNPs. For a given concentration of PSA (and AuNPs) the conductance increased with the increase of the gate voltage. For a given gate voltage, the conductance was observed to increase for increasing concentration of PSA. This allowed proposing a calibration line for the biosensor, which is valid from a clinically relevant range of 0.1 ng/mLWe acknowledge MSC funding provided by the European Commission through FP7 grant THINFACE (ITN GA 607232) and from Ministerio de Economía y Competitividad, Spain, through grant SPECTRASENSE (RTC-2017-6311-1

Quality of life and not health status improves after major amputation in the elderly critical limb ischemia patient

Objectives A patient-oriented appraisal of treatment has become extremely important, particularly in elderly patients with critical limb ischaemia (CLI). Quality of life (QoL) is an important patient-reported outcome in vascular surgery. Frequently, the physical domain of QoL questionnaires represents an ‘objective’ evaluation of performing activities, which is expected to be impaired after major limb amputation. However, an objective appraisal of physical function is an assessment of health status (HS) and not of QoL. Little is known about the subjective appraisal of physical health (QoL). The goal of this study was to evaluate, prospectively, QoL in relation to HS in elderly CLI patients undergoing major limb amputation. Methods Patients suffering from CLI aged 70 years or older were included in a prospective observational cohort study with a follow-up period of 1 year. Patients were divided according to having had an amputation or not. The World Health Organization Quality Of Life-BREF (WHOQOL-BREF) was used to asses QoL. The 12-Item Short Form Health Survey (SF-12) was used to measure HS. These self-reported questionnaires were completed five times during follow-up.ResultsTwo-hundred patients were included of whom 46 underwent a major limb amputation within one year. Amputees had a statistically significant improvement of their physical QoL after six months (14.0 vs. 9.0 (95% CI -7.84;-1.45),p = 0.005) and after a one-year follow-up (14.0 vs. 9.0 (95% CI -9.58;-1.46),p = 0.008). They did not however show any statistically significant difference in HS. For non-amputees, both physical QoL and HS improved. An instant statistically significant improvement of the physical QoL appeared 1 week after inclusion (12.0 vs. 10.9 (95% CI -1.57;-0.63),p<0.001). Similarly, statistically significant improvement in the physical HS first occurred at 1 week follow-up (29.0 vs. 28.9 (95% CI -5.78; −2.23),p = 0.003). Conclusions There is a clear difference between patients' functioning (HS) and the patients' appraisal of functioning (QoL). In elderly CLI patients, this study clearly suggests a discrepancy between the physical QoL (WHOQOL-BREF) and HS (SF-12) measurements in vascular amputees. This raises the question, which outcome measurement is the most relevant for elderly CLI patients. Individual treatment goals should be kept in mind when assessing the HS or QoL outcome of patients undergoing hospital care. With respect to shared decision making, distinctive and subjective QoL questionnaires, like the WHOQOL-BREF, provide a very important outcome measurement and should be used in future research

Pseudoentropic Isometries: A New Framework for Fuzzy Extractor Reusability

Fuzzy extractors (Dodis \textit{et al.}, Eurocrypt 2004) turn a noisy secret into a stable, uniformly distributed key. \textit{Reusable} fuzzy extractors remain secure when multiple keys are produced from a single noisy secret (Boyen, CCS 2004). Boyen proved that any information-theoretically secure reusable fuzzy extractor is subject to strong limitations. Simoens \textit{et al.} (IEEE S\&P, 2009) then showed deployed constructions suffer severe security breaks when reused. Canetti \textit{et al.} (Eurocrypt 2016) proposed using computational security to sidestep this problem. They constructed a computationally secure reusable fuzzy extractor for the Hamming metric that corrects a \emph{sublinear} fraction of errors. We introduce a generic approach to constructing reusable fuzzy extractors. We define a new primitive called a \emph{reusable pseudoentropic isometry} that projects an input metric space to an output metric space. This projection preserves distance and entropy even if the same input is mapped to multiple output metric spaces. A reusable pseudoentropy isometry yields a reusable fuzzy extractor by 1) randomizing the noisy secret using the isometry and 2) applying a traditional fuzzy extractor to derive a secret key. We propose reusable pseudoentropic isometries for the set difference and Hamming metrics. The set difference construction is built from composable digital lockers (Canetti and Dakdouk, Eurocrypt 2008) yielding the first reusable fuzzy extractor that corrects a {\it linear} fraction of errors. For the Hamming metric, we show that the second construction of Canetti \textit{et al.} (Eurocrypt 2016) can be seen as an instantiation of our framework. In both cases, the pseudoentropic isometry\u27s reusability requires noisy secrets distributions to have entropy in each symbol of the alphabet. Lastly, we implement our set difference solution and describe two use cases

Synthetic lethality between PAXX and XLF in mammalian development.

PAXX was identified recently as a novel nonhomologous end-joining DNA repair factor in human cells. To characterize its physiological roles, we generated Paxx-deficient mice. Like Xlf-/- mice, Paxx-/- mice are viable, grow normally, and are fertile but show mild radiosensitivity. Strikingly, while Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency, Paxx/Xlf double-knockout mice display embryonic lethality associated with genomic instability, cell death in the central nervous system, and an almost complete block in lymphogenesis, phenotypes that closely resemble those of Xrcc4-/- and Lig4-/- mice. Thus, combined loss of Paxx and Xlf is synthetic-lethal in mammals.Research in S.P.J.’s laboratory is funded by Cancer Research UK (CRUK) program grant number C6/A11224, the European Research Council, and the European Community Seventh Framework Programme grant agreement number HEALTH-F2-2010-259893 (DDResponse). Core funding is provided by CRUK (C6946/A14492) and the Wellcome Trust (WT092096). S.P.J. receives his salary from the University of Cambridge, UK, supplemented by CRUK. L.D.’s laboratory is funded by the Institut Pasteur as well as the European Research Council (ERC) under starting grant agreement number 310917. D.J.A.’s laboratory is supported by CRUK and the Wellcome Trust. A.N.B. is supported by a CRUK Career Development Fellowship (C29215/A20772).This is the final version of the article. It first appeared from Cold Spring Harbor Laboratory Press via https://doi.org/10.1101/gad.290510.11

Natural Killer Cells Exhibit a Peculiar Phenotypic Profile in Systemic Sclerosis and Are Potent Inducers of Endothelial Microparticles Release

The pathophysiology of systemic sclerosis (SSc) involves early endothelial and immune activation, both preceding the onset of fibrosis. We previously identified soluble fractalkine and circulating endothelial microparticles (EMPs) as biomarkers of endothelial inflammatory activation in SSc. Fractalkine plays a dual role as a membrane-bound adhesion molecule expressed in inflamed endothelial cells (ECs) and as a chemokine involved in the recruitment, transmigration, and cytotoxic activation of immune cells that express CX3CR1, the receptor of fractalkine, namely CD8 and γδ T cells and natural killer (NK) cells. We aimed to quantify circulating cytotoxic immune cells and their expression of CX3CR1. We further investigated the expression profile of NK cells chemokine receptors and activation markers and the potential of NK cells to induce EC activation in SSc. We performed a monocentric study (NCT 02636127) enrolling 15 SSc patients [15 females, median age of 55 years (39–63), 11 limited cutaneous form and 4 diffuse] and 15 healthy controls. Serum fractalkine levels were significantly increased in SSc patients. Circulating CD8 T cells numbers were decreased in SSc patients with no difference in their CX3CR1 expression. Circulating γδ T cells and NK cells numbers were preserved. CX3CR1 expression in CD8 and γδ T cells did not differ between SSc patients and controls. The percentage and level of CX3CR1 expression in NK cells were significantly lowered in SSc patients. Percentages of CXCR4, NKG2D, CD69-expressing NK cells, and their expression levels were decreased in NK cells. Conversely, CD16 level expression and percentages of CD16+ NK cells were preserved. The exposure of human microvascular dermic EC line (HMVEC-d) to peripheral blood mononuclear cells resulted in similar NK cells degranulation activity in SSc patients and controls. We further showed that NK cells purified from the blood of SSc patients induced enhanced release of EMPs than NK cells from controls. This study evidenced a peculiar NK cells phenotype in SSc characterized by decreased chemokine and activation receptors expression, that might reflect NK cells involvement in the pathogenic process. It also highlighted the role of NK cells as a potent mechanism inducing endothelial activation through enhanced EMPs release

Pour une démocratie socio-environnementale : cadre pour une plate-forme participative « transition écologique »

Contribution publiée in Penser une démocratie alimentaire Volume II – Proposition Lascaux entre ressources naturelles et besoins fondamentaux, F. Collart Dutilleul et T. Bréger (dir), Inida, San José, 2014, pp. 87-111.International audienceL’anthropocène triomphant actuel, avec ses forçages environnementaux et sociaux, est à l’origine de l’accélération des dégradations des milieux de vie sur Terre et de l’accentuation des tensions sociales et géopolitiques. Passer à un anthropocène de gestion équitable, informé et sobre vis-à-vis de toutes les ressources et dans tous les secteurs d’activité (slow anthropocene), impose une analyse préalable sur l’ensemble des activités et des rapports humains. Cette transition dite « écologique », mais en réalité à la fois sociétale et écologique, est tout sauf un ajustement technique de secteurs dits prioritaires et technocratiques. Elle est avant tout culturelle, politique et philosophique au sens propre du terme. Elle est un horizon pour des trajectoires de développement humain, pour des constructions sociales et économiques, censées redéfinir socialement richesse, bien-être, travail etc. La dénomination « transition écologique » est largement véhiculée, mais ses bases conceptuelles ne sont pas entièrement acquises ni même élaborées. Dans ce contexte, les étudiants en première année de Master BioSciences à l’Ecole Normale Supérieure (ENS) de Lyon ont préparé une première étude analytique de ce changement radical et global de société pour mieux comprendre dans quelle société ils souhaitent vivre, en donnant du sens aux activités humaines présentes et à venir. Une trentaine de dossiers sur divers secteurs d’activités et acteurs de la société ont été produits et ont servis de support à cette synthèse. Plus largement, le but est de construire un socle conceptuel et une plate-forme de travail sur lesquels les questions de fond, mais aussi opérationnelles, peuvent être posées et étudiées en permanence. Cette démarche participative est ouverte à la collectivité sur le site http://institutmichelserres.ens-lyon.fr/