Ungewöhnliche Solidaritäten

Mujeres Creando, das mit Frauen, die erschaffen, übersetzt werden kann, definiert sich als soziale Bewegung feministischer Frauen in Bolivien. Ihr Aktivismus zeichnet sich u.a. durch Straßenaktionen, politische Graffitis und die im eigenen Gemeinschaftshaus erbrachten Dienstleistungen aus. Diese konkrete politische Arbeit wird mit einem langfristigen Ziel verbunden: Durch das Eingehen von Solidaritäten mit diversen Frauen soll ein gemeinsames Erkenntnissubjekt der Frauen erschaffen und die bestehende soziale Ordnung verändert werden. Diese Allianzen bauen auf dem Heterogenitätskonzept, d.h. der Anerkennung der Differenzen zwischen Frauen auf, um den verschiedenen Situierungen der Frauen gerecht zu werden und somit vielen Frauen Identifikationsmöglichkeit mit der gemeinsamen Bewegung zu bieten. Die Frage welches Potential das Heterogenitätskonzept der Mujeres Creando zum Aufbrechen der bolivianischen Dominanzkultur besitzt, steht im Mittelpunkt der vorliegenden Arbeit. Die Dominanzkultur hat sich im Laufe der Kolonialisierung entwickelt und zeichnet sich durch strukturellen Rassismus und die angenommene Minderwertigkeit der indigenen Bevölkerung aus, was eine starke Interdependenz zwischen den Kategorien gender, ‚Ethnizität’, ‚Klasse’ und sozialen Ansehen hervorgebracht hat. Ausgehend von einem interdisziplinären Forschungsansatz und der Beschäftigung mit der Differenzdebatte in der Feministischen Anthropologie wird die theoretische Grundlage dieser Arbeit geschaffen. In der Feldforschung erhobene empirische Daten (Interviews und Feldnotizen) sowie von Mujeres Creando verfasste theoretische Texte und aus dem Internet entnommene Interviews mit den Aktivistinnen werden nach Phillip Mayrings Inhaltsanalyse interpretiert und ausgewertet. Durch den Einbezug der Ergebnisse aus der teilnehmenden Beobachtung können Widersprüche zwischen den theoretischen Konzepten der Mujeres Creando und deren Umsetzung in die Praxis festgestellt werden

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Single-cell RNA-sequencing (scRNA-seq) facilitates identification of new cell types and gene regulatory networks as well as dissection of the kinetics of gene expression and patterns of allele-specific expression. However, to facilitate such analyses, separating biological variability from the high level of technical noise that affects scRNA-seq protocols is vital. Here we describe and validate a generative statistical model that accurately quantifies technical noise with the help of external RNA spike-ins. Applying our approach to investigate stochastic allele-specific expression in individual cells, we demonstrate that a large fraction of stochastic allele-specific expression can be explained by technical noise, especially for lowly and moderately expressed genes: we predict that only 17.8% of stochastic allele-specific expression patterns are attributable to biological noise with the remainder due to technical noise

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Nature Communications 6: Article number: 8687 (2015); Published: 22 October 2015; Updated: 11 January 2016. The original version of this Article contained an error in the spelling of the author Tomislav Ilicic, which was incorrectly given as Tomislav Illicic. This has now been corrected in both the PDF and HTML versions of the Article.</jats:p

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive complex is to dampen expression of these PRC-active genes. However, it is unclear how this flipping between chromatin states alters the kinetics of transcription. Here, we integrate histone modifications and RNAPII states derived from bulk ChIP-seq data with single-cell RNA-sequencing data. We find that Polycomb repressive complex-active genes have greater cell-to-cell variation in expression than active genes, and these results are validated by knockout experiments. We also show that PRC-active genes are clustered on chromosomes in both two and three dimensions, and interactions with active enhancers promote a stabilization of gene expression noise. These findings provide new insights into how chromatin regulation modulates stochastic gene expression and transcriptional bursting, with implications for regulation of pluripotency and development.Polycomb repressive complexes modify histones but it is unclear how changes in chromatin states alter kinetics of transcription. Here, the authors use single-cell RNAseq and ChIPseq to find that actively transcribed genes with Polycomb marks have greater cell-to-cell variation in expression

Novel Pathogenic PRSS1 Variant p.Glu190Lys in a Case of Chronic Pancreatitis

Mutations in the PRSS1 (serine protease 1) gene encoding human cationic trypsinogen cause hereditary pancreatitis or may be associated with sporadic chronic pancreatitis. The mutations exert their pathogenic effect either by increasing intra-pancreatic trypsinogen activation (trypsin pathway) or by causing proenzyme misfolding and endoplasmic reticulum stress (misfolding pathway). Here we report a novel heterozygous c.568G&gt;A (p.Glu190Lys) variant identified in a case with chronic pancreatitis. The parents of the index patient had no history of pancreatitis but were unavailable for genetic testing. Functional characterization revealed 2.5-fold increased autoactivation of the mutant trypsinogen relative to wild type. Unlike many other clinically relevant PRSS1 mutations, p.Glu190Lys did not alter the chymotrypsin C (CTRC)-dependent degradation of trypsinogen nor did it increase CTRC-mediated processing of the trypsinogen activation peptide. Cellular secretion of the mutant protein was unchanged indicating normal folding behavior. Based on the genetic and functional evidence, we classify the p.Glu190Lys PRSS1 variant as likely pathogenic, which stimulates autoactivation of cationic trypsinogen independently of CTRC

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

SummaryEmbryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state. Overall levels of intercellular gene expression heterogeneity are comparable across the three conditions. However, this masks variable expression of pluripotency genes in serum cells and homogeneous expression in 2i and a2i cells. Additionally, genes related to the cell cycle are more variably expressed in the 2i and a2i conditions. Mining of our dataset for correlations in gene expression allowed us to identify additional components of the pluripotency network, including Ptma and Zfp640, illustrating its value as a resource for future discovery

Classification of low quality cells from single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical research. One of the key challenges is to ensure that only single, live cells are included in downstream analysis, as the inclusion of compromised cells inevitably affects data interpretation. Here, we present a generic approach for processing scRNA-seq data and detecting low quality cells, using a curated set of over 20 biological and technical features. Our approach improves classification accuracy by over 30 % compared to traditional methods when tested on over 5,000 cells, including CD4+ T cells, bone marrow dendritic cells, and mouse embryonic stem cells

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

BACKGROUND: Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell surface markers. Recent studies have identified significant cellular heterogeneities in the HSC compartment with subsets of HSCs displaying lineage bias. We previously discovered that the transcription factor Bcl11a has critical functions in the lymphoid development of the HSC compartment. RESULTS: In this report, we employ single-cell transcriptomic analysis to dissect the molecular heterogeneities in HSCs. We profile the transcriptomes of 180 highly purified HSCs (Bcl11a (+/+) and Bcl11a (-/-)). Detailed analysis of the RNA-seq data identifies cell cycle activity as the major source of transcriptomic variation in the HSC compartment, which allows reconstruction of HSC cell cycle progression in silico. Single-cell RNA-seq profiling of Bcl11a (-/-) HSCs reveals abnormal proliferative phenotypes. Analysis of lineage gene expression suggests that the Bcl11a (-/-) HSCs are constituted of two distinct myeloerythroid-restricted subpopulations. Remarkably, similar myeloid-restricted cells could also be detected in the wild-type HSC compartment, suggesting selective elimination of lymphoid-competent HSCs after Bcl11a deletion. These defects are experimentally validated in serial transplantation experiments where Bcl11a (-/-) HSCs are myeloerythroid-restricted and defective in self-renewal. CONCLUSIONS: Our study demonstrates the power of single-cell transcriptomics in dissecting cellular process and lineage heterogeneities in stem cell compartments, and further reveals the molecular and cellular defects in the Bcl11a-deficient HSC compartment

miTuner - a kit for microRNA based gene expression tuning in mammalian cells

The purpose of this RFC is to introduce a modular expression tuning kit for use in mammalian cells. The kit enables the regulation of the gene expression of any gene of interest (GOI) based on synthetic microRNAs, endogenous microRNAs or a combination of both