Dissecting stem cell differentiation using single cell expression profiling.

Many assumptions about the way cells behave are based on analyses of populations. However, it is now widely recognized that even apparently pure populations can display a remarkable level of heterogeneity. This is particularly true in stem cell biology where it hinders our understanding of normal development and the development of strategies for regenerative medicine. Over the past decade technologies facilitating gene expression analysis at the single cell level have become widespread, providing access to rare cell populations and insights into population structure and function. Here we review the contributions of single cell biology to understanding stem cell differentiation so far, both as a new methodology for defining cell types and a tool for understanding the complexities of cellular decision-making.Research in the authors’ laboratories is supported by the Medical Research Council, Biotechnology and Biological Sciences Research Council, Bloodwise, the Leukemia and Lymphoma Society, a Wellcome Trust Strategic Award (Tracing Early Mammalian Lineage Decisions by Single Cell Genomics) and core support grants by the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust - MRC Cambridge Stem Cell Institute.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.ceb.2016.08.00

Le collège comme espace de structuration des bandes d’adolescents dans les quartiers populaires : le poids de la ségrégation scolaire

Cet article s’intéresse à la place du collège comme espace de structuration des bandes d’adolescents dans les quartiers populaires. L’étude de la répartition des élèves membres de bandes sur deux ans fait apparaître leur concentration dans un nombre très limité de classes de l’établissement. La mise en place de cette politique aboutit à une forme de ségrégation interne qui participe fortement à la construction d’une expérience collégienne douloureuse marquée par une détérioration du climat scolaire et une éthnicisation des rapports scolaires fortement structurants pour les bandes d’adolescents.This article addresses the role of the “college” (junior high school) as a place in which gangs of teenagers are structured in working-class districts. A study of the distribution of pupils who were gang members over two years showed that they were concentrated in a very limited number of classes in the school. The introduction of this policy leads to a form of internal segregation which plays a powerful role in constructing a painful school experience marked by a deterioration of the school climate and an ethnicisation of school relations which contribute greatly to the formation of youth gangs.Este artículo se interesa por el lugar del colegio como espacio de estructuración de las pandillas de adolescentes en los barrios populares. El estudio de la repartición de los alumnos miembros de una pandilla durante dos años pone de manifiesto su concentración en un número muy limitado de clases del establecimiento. La instalación de esta política conduce a una forma de segregación interna que participa intensamente en la construcción de una experiencia colegial dolorosa marcada por una deterioración del clima escolar y una etnicización de las relaciones escolares fuertemente estructurantes para las pandillas de adolescentes.* Das Collège betrifft in Frankreich alle Schüler zwischen 11 und 15 und entspricht etwa den Klassen 6 bis 9 im deutschen Schulsystem.Dieser Artikel befasst sich mit dem Platz des Collège als Feld der Strukturierung für Jugendlichenbanden in Arbeitervierteln. Eine zwei Jahre lange Untersuchung über die Verteilung der Schüler, die Mitglieder einer solchen Bande sind, lässt erkennen, dass sie sich in einer geringen Anzahl von Klassen konzentrieren. Diese Politik führt zu einer Form der internen Trennung, die zum größten Teil zur Bildung einer negativen Erfahrung am Collège beiträgt, die von einer Verschlechterung des Schulklimas und von einer Verethnisierung der Schulbeziehungen geprägt sind, beide Faktoren üben wiederum starken Einfluß auf die Strukturierung der Jugendlichenbanden

Processing, visualising and reconstructing network models from single-cell data.

New single-cell technologies readily permit gene expression profiling of thousands of cells at single-cell resolution. In this review, we will discuss methods for visualisation and interpretation of single-cell gene expression data, and the computational analysis needed to go from raw data to predictive executable models of gene regulatory network function. We will focus primarily on single-cell real-time quantitative PCR and RNA-sequencing data, but much of what we cover will also be relevant to other platforms, such as the mass cytometry technology for high-dimensional single-cell proteomics.S.W is supported by a Microsoft Research PhD Scholarship.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/icb.2015.10

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data.

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics.This work was supported by: Royal Society Research Fellowship, Marshall Scholarship, Medical Research Council, the Leukemia and Lymphoma Society and core support grants from the Wellcome Trust to the Cambridge Institute for Medical Research and the Wellcome Trust and MRC Cambridge Stem Cell Institute.This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pcbi.100507

BNC1 regulates cell heterogeneity in human pluripotent stem cell derived-epicardium

The murine developing epicardium heterogeneously expresses the transcription factors TCF21 and WT1. Here, we show that this cell heterogeneity is conserved in human epicardium, regulated by BNC1 and associated with cell fate and function. Single cell RNAseq of epicardium derived from human pluripotent stem cells (hPSC-epi) revealed that distinct epicardial sub-populations are defined by high levels of expression for the transcription factors BNC1 or TCF21. WT1+ cells are included in the BNC1+ population, which was confirmed in human foetal hearts. THY1 emerged as a membrane marker of the TCF21 population. We show that THY1+ cells can differentiate into cardiac fibroblast (CF) and smooth muscle cells (SMC), while THY1-cells were predominantly restricted to SMC. Knocking down BNC1 during the establishment of the epicardial populations resulted in a homogeneous, predominantly, TCF21high population. Network inference methods using transcriptomic data from the different cell lineages derived from the hPSC-epi, delivered a core transcriptional network organized around WT1, TCF21 and BNC1. This study is a step towards engineering sub-populations of epicardial cells with selective biological activities and unveils a list of epicardial regulators.This work was supported by the British Heart Foundation Oxbridge Centre for Regenerative Medicine RM/13/3/30159 and RM/17/2/33380 (LG, SS) and BHF grants FS/14/59/31282 (SAM), FS/13/29/30024 and FS/18/46/33663 (SS). SS was also supported by the British Heart Foundation Centre for Cardiovascular Research Excellence. Core support was provided by the Wellcome-MRC Cambridge Stem Cell Institute (203151/Z/16/Z) and the Cambridge Hospitals National Institute for Health Research Biomedical Research Centre funding (SS). VM was supported by a Wellcome PhD studentship as part of the Stem Cell Institute PhD programme. Research in the Gottgens group is supported by programmatic funding from Wellcome, CRUK and Bloodwise. Single cell experiments were supported through an MRC Clinical Research Infrastructure award. NL was supported by the Biotechnology and Biological Sciences Research Council (Institute Strategic Programmes BBS/E/B/000C0419 and BBS/E/B/000C0434). DS was supported by an ERASMUS+ internship. WGB was supported from the Stroke Association (TSA 2016/02 PP11_Sinha)

Seeking out the Remote and the Divine: Story Paradigms Shaping Second Sophistic 'Lives'

This thesis arose from the observation that two sorts of journeys commonly described in Second Sophistic literature – to religious and, in particular, oracular sites, and to the 'end of the earth' – are rarely considered together, although they have in common the liminal nature of their destinations. Like oracular sites, the boundaries of the earth were numinous, closer to the gods than the places we know, their inhabitants superior or in touch with the divine. The thesis proposes that, and explores the ways in which, tales of journeys of both kinds were regularly used by Second Sophistic writers to assert – or deny – the superior or even divine nature of their protagonists. Here, 'Second Sophistic writers' are identified simply as writers active in the period c. 60-230 CE

Generation of multipotent foregut stem cells from human pluripotent stem cells

Human pluripotent stem cells (hPSCs) could provide an infinite source of clinically relevant cells with potential applications in regenerative medicine. However, hPSC lines vary in their capacity to generate specialized cells, and the development of universal protocols for the production of tissue-specific cells remains a major challenge. Here, we have addressed this limitation for the endodermal lineage by developing a defined culture system to expand and differentiate human foregut stem cells (hFSCs) derived from hPSCs. hFSCs can self-renew while maintaining their capacity to differentiate into pancreatic and hepatic cells. Furthermore, near-homogenous populations of hFSCs can be obtained from hPSC lines which are normally refractory to endodermal differentiation. Therefore, hFSCs provide a unique approach to bypass variability between pluripotent lines in order to obtain a sustainable source of multipotent endoderm stem cells for basic studies and to produce a diversity of endodermal derivatives with a clinical value

Reconstructing Gene Regulatory Networks That Control Hematopoietic Commitment.

Hematopoietic stem cells (HSCs) reside at the apex of the hematopoietic hierarchy, possessing the ability to self-renew and differentiate toward all mature blood lineages. Along with more specialized progenitor cells, HSCs have an essential role in maintaining a healthy blood system. Incorrect regulation of cell fate decisions in stem/progenitor cells can lead to an imbalance of mature blood cell populations-a situation seen in diseases such as leukemia. Transcription factors, acting as part of complex regulatory networks, are known to play an important role in regulating hematopoietic cell fate decisions. Yet, discovering the interactions present in these networks remains a big challenge. Here, we discuss a computational method that uses single-cell gene expression data to reconstruct Boolean gene regulatory network models and show how this technique can be applied to enhance our understanding of transcriptional regulation in hematopoiesis.Work in the author’s laboratory is supported by grants from the Wellcome, Bloodwise, Cancer Research UK, NIH-NIDDK and core support grants by the Wellcome to the Cambridge Institute for Medical Research and Wellcome & MRC Cambridge Stem Cell Institute. F.K.H. is a recipient of a Medical Research Council PhD Studentship

Développement d’un appareil portable de diffraction et fluorescence des rayons X pour l’analyse non-destructive des œuvres d’art

Au début des années 2000, l’impulsion de contrats européens a entraîné le C2RMF dans la conception et la construction d’un appareil portable de fluorescence et diffraction des rayons X (FRX-DRX). Les choix techniques concernant la source et les détecteurs ont conduit à un appareil robuste, qui a été utilisé dans de nombreux pays d’Europe, à la source d’une trentaine de publications dans des revues scientifiques.In the early 2000s, the stimulus of European contracts led the C2RMF teams to design and build a portable X-ray diffraction/X-ray fluorescence (XRD/XRF) device. The technical choices made concerning the source and detectors resulted in a robust device, which has been used in several European countries and produced about thirty or so articles published in scientific journals