53 Works

Identification of long noncoding RNAs in regulation of cell division.

Lovorka Stojic
Long noncoding RNAs (lncRNAs) regulate many biological processes and have been implicated in development and disease pathogenesis. The exact function for the large majority of lncRNAs is still unknown. To address whether lncRNAs could play a role in cell division, we combined a microscopy-based high-content RNAi screen with dedicated image analysis workflows to identify lncRNAs that regulate mitotic progression, chromosome segregation and cytokinesis. By targeting over 2000 lncRNAs in HeLa cells, we discovered an assortment...

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Jonas Hartmann
3D confocal imaging of fixed samples of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP and stained for pea3 mRNA using single molecule Fluorescence In-Situ Hybridization (smFISH).

HDBR Atlas: Gene Expression in Early Human Development

Janet Kerwin, Yiya Yang, Paloma Merchan, Subrot Sarma, Jessica Thompson, Xunxian Wang, Juan Sandoval, Luis Puelles, Richard Baldock & Susan Lindsay
Gene expression studies in early human development from 3 to 17 post conceptional weeks (PCW).

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Jonas Hartmann
3D confocal live imaging of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP for segmentation and optionally with one of several additional labels.

Molecular determinants of large cargo transport into the nucleus

Joana Caria
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Even very large cargoes such as many pathogens, mRNAs and pre-ribosomal subunits can pass the NPC intact. Compared to small import complexes, for such large cargoes >15 nm there is very little quantitative understanding of the mechanism for efficient transport, the role of multivalent binding to nuclear transport receptors via nuclear localisation sequences (NLSs) and effects of size differences. Here, we assayed nuclear import...

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Primary image-based screen of 1,278 mostly FDA-approved, off-patent small molecules, collected in the Prestwick Chemical Library for inhibitors of Human adenovirus infection

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Human adenovirus infected Z' plates in biological duplicates consisting of 192 technical replicates of the solvent control DMSO and positive control DFT to confirm assay quality

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Thomas Julou
We use quantitative time-lapse microscopy combined with microfluidics to analyse the induction dynamics of the lac operon in single bacteria cells.

A semi-automated intestinal organoid screening method demonstrates epigenetic control of epithelial maturation

Jenny Ostrop
The intestinal epithelium maintains an important barrier throughout life. It consists of several epithelial cell lineages that are derived from LGR5+ intestinal stem cells. Although epigenetic regulation of embryonic stem cell differentiation is well established, its role in adult stem cell systems such as the intestinal epithelium is still undefined. Yet, targeting of epigenetic regulatory enzymes may be relevant for new therapeutics, for example in cancer treatment. Here, we combine a newly established organoid toolbox...

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

SARS-COV-2 drug repurposing - Caco2 cell line

Bernhard Ellinger
To identify possible candidates for progression towards clinical studies against SARS-CoV-2, we screened a well-defined collection of 5632 compounds including 3488 compounds which have undergone clinical investigations (marketed drugs, phases 1 -3, and withdrawn) across 600 indications. Compounds were screened for their inhibition of viral induced cytotoxicity using the human epithelial colorectal adenocarcinoma cell line Caco-2 and a SARS-CoV-2 isolate. The primary screen of 5632 compounds gave 271 hits. A total of 64 compounds with...

Time-resolved imaging-based CRISPRi screening method.

Johan Elf

Graph-based description of tertiary lymphoid organs (TLOs) at single-cell.

Friedrich Feuerhake
Object-oriented image analysis and graph-based description of the spatial context of B- and T-lymphocytes were performed to reflect the degree of organization in lymphocyte accumulations and their similarity with TLOs. This study addresses the need to detect and reproducibly classify immune cell infiltrates in histopathological sections. We propose complementing observer-dependent approaches of immune cell evaluation in microscopy images with reproducible measures for spatial composition of lymphocytic infiltrates.

Visual programming for structural assessment of out-of-plane mechanisms in historic masonry structures

Marco Francesco Funari & Saverio Spadea
A visual script created during the work for the paper ‘Visual programming for structural assessment of out-of-plane mechanisms in historic masonry structures’, published by Funari, Spadea et al. (2020) in the Journal of Building Engineering. A support guide document to approach the visual scripting for structural assessment of historic masonry structures. The guide shows the practical aspects of the methods theoretically developed in the paper. The dataset of a benchmark case study suitable to test...

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

Ezequiel Miron
Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and...

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Primary image-based screen of 1,278 mostly FDA-approved, off-patent small molecules, collected in the Prestwick Chemical Library for inhibitors of Human adenovirus infection

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

Ezequiel Miron
Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and...

SARS-COV-2 drug repurposing - Caco2 cell line

Bernhard Ellinger
To identify possible candidates for progression towards clinical studies against SARS-CoV-2, we screened a well-defined collection of 5632 compounds including 3488 compounds which have undergone clinical investigations (marketed drugs, phases 1 -3, and withdrawn) across 600 indications. Compounds were screened for their inhibition of viral induced cytotoxicity using the human epithelial colorectal adenocarcinoma cell line Caco-2 and a SARS-CoV-2 isolate. The primary screen of 5632 compounds gave 271 hits. A total of 64 compounds with...

Tales of 1,008 Small Molecules: Phenomic Profiling through Live-cell Imaging in a Panel of Reporter Cell Lines

Steffen Jaensch
To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and tool compounds manually annotated to 218 unique MoAs and an additional 169 natural products, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. Phenomic profiling can be used for...

Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif

Robert Brewster
Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its...

Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif

Robert Brewster
Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its...

Using a same-different matching task to determine the viability of parallel lexical processing: Measuring reaction time and error rates.

Laura J Wakeford & Wayne S Murray
Reaction time and error rate means for each experimental condition averaged over the set of items within the condition (for the by-subjects analysis) and over the subjects tested on that condition (for the by-items analysis). The initial sheet of this Excel document provides instruction on how to read and interpret the layout of the following sheets.

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Human adenovirus infected Z' plates in biological duplicates consisting of 192 technical replicates of the solvent control DMSO and positive control DFT to confirm assay quality.

Registration Year

  • 2020
    53

Resource Types

  • Image
    45
  • Dataset
    8

Affiliations

  • University of Massachusetts Medical School
    3
  • RIKEN
    2
  • Institute for Research in Biomedicine
    2
  • Memorial Sloan Kettering Cancer Center
    2
  • Institute of Biomedical Research of Barcelona
    2
  • Institució Catalana de Recerca i Estudis Avançats
    2
  • University of Toronto
    2
  • University Hospital Frankfurt
    2
  • Fraunhofer Institute for Molecular Biology and Applied Ecology
    2
  • Goethe University Frankfurt
    2