CellProfiler™: Free, Versatile Software for Automated Biological Image Analysis

Lamprecht, Michael R.; Sabatini, David M.; Carpenter, Anne E.

doi:10.2144/000112257

Cited by 822 publications

(639 citation statements)

References 20 publications

Supporting

Mentioning

636

Contrasting

Unclassified

Order By: Relevance

“…Fat body nuclear diameter and wing imaginal disc volume were measured from DAPI-stained, fixed tissues imaged by confocal microscopy. Adult wings were imaged by light microscopy and area measurements were performed using a custom pipeline in CellProfiler [58]. Detailed methods are provided in [8].…”

Section: Ssd Is Regulated Differently In Larval and Imaginal Tissuesmentioning

confidence: 99%

Sex-lethal in neurons controls female body growth inDrosophila

Sawala

Gould

2018

Fly

View full text Add to dashboard Cite

Sexual size dimorphism (SSD), a sex difference in body size, is widespread throughout the animal kingdom, raising the question of how sex influences existing growth regulatory pathways to bring about SSD. In insects, somatic sexual differentiation has long been considered to be controlled strictly cell-autonomously. Here, we discuss our surprising finding that in Drosophila larvae, the sex determination gene Sex-lethal (Sxl) functions in neurons to non-autonomously specify SSD. We found that Sxl is required in specific neuronal subsets to upregulate female body growth, including in the neurosecretory insulin producing cells, even though insulin-like peptides themselves appear not to be involved. SSD regulation by neuronal Sxl is also independent of its known splicing targets, transformer and msl-2, suggesting that it involves a new molecular mechanism. Interestingly, SSD control by neuronal Sxl is selective for larval, not imaginal tissue types, and operates in addition to cell-autonomous effects of Sxl and Tra, which are present in both larval and imaginal tissues. Overall, our findings add to a small but growing number of studies reporting non-autonomous, likely hormonal, control of sex differences in Drosophila, and suggest that the principles of sexual differentiation in insects and mammals may be more similar than previously thought.

show abstract

Section: Ssd Is Regulated Differently In Larval and Imaginal Tissuesmentioning

confidence: 99%

Sex-lethal in neurons controls female body growth inDrosophila

Sawala

Gould

2018

Fly

View full text Add to dashboard Cite

show abstract

“…Images were analyzed for biofilm area coverage using CellProfiler. 38 The pipeline consisted of load images, enhance edges, apply threshold, identify primary objects, measure area occupied and export spreadsheet. The Student's t-test was applied with confidence level 0.05 and confidence interval of 99% to select the images.…”

Section: Cell Aggregation Assaymentioning

confidence: 99%

“…Since phase-contrast microscopy enables direct visualization of cell aggregates, we implement a pipeline for detection and measurement of relative aggregate-covered area (RACA) using CellProfiler software. 38 RACA is a good biofilm quantification index since it enables the evaluation of cell aggregate population and size distributions simultaneously. IPTG concentration of 0.1 mM consistently yielded cell aggregates ranging from 5 to 50 µm.…”

Section: Functional Tests On the Selected Compounds From The Virtual mentioning

confidence: 99%

Identification of Anti-Inflammatory and Anti-Hypertensive Drugs as Inhibitors of Bacterial Diguanylate Cyclases

Wiggers¹,

Crusca²,

Silva³

et al. 2017

J. Braz. Chem. Soc.

View full text Add to dashboard Cite

Biofilms are widely present in many human chronic infections, often more resistant to treatment with antibiotics. Bacterial diguanylate cyclases (DGCs) synthesize cyclic dimeric guanosine monophosphate (c-di-GMP) from two guanosine-5'-triphosphate (GTP) molecules. c-di-GMP is a central second messenger controlling biofilm formation, turning this class of enzymes an attractive target to prevent and disrupt biofilms of pathogenic bacteria. Here, we apply an in silico ligand-and target-based hybrid method to screen potential DGC inhibitors from an FDA-approved drug databank. Mass spectrometry assays confirmed that seven screened compounds selectively bound to the GTP active site of P. aeruginosa WspR GGDEF domain. Four out of those, including the anti-inflammatory sulfasalazine and the anti-hypertensive eprosartan, inhibited distinct DGCs (P. aeruginosa WspR and E. coli YdeH) in the micromolar range. Sulfasalazine and eprosartan reduced aggregation in solution of E. coli overexpressing WspR or YdeH. Similar anti-aggregation effects were also observed for sulfasalazine-related anti-inflammatory drugs sulfadiazine and sulfathiazole, the latter a previously described anti-biofilm agent. The optimized pharmacokinetic properties and toxicological profiles of the DGC inhibitors could be promising candidates for new anti-microbial agents based on the drug reposition strategy.Keywords: c-di-GMP, diguanylate cyclase enzymes, bacterial biofilm, virtual screening, drug repositioning IntroductionBacterial biofilms, a multicellular community encased in an extracellular matrix, are commonly related to persistent infections, usually less susceptible to antibiotic treatments when compared to planktonic cells. [1][2][3] According to the National Institute of Health, 4 up to 80% of human bacterial infections involve biofilm-associated microorganisms. For instance, biofilm formation plays a crucial role in microbe pathogenicity such as Legionnaire's disease, endocarditis, pneumonia accompanied by cystic fibrosis and infections of urogenital and gastrointestinal tracts. 5,6 Furthermore, biofilm infections promote devastating effects on medical device implanted and immunocompromised individuals, representing a major medical and economic predicament. 7 The burden on public health due to chronic biofilm contaminations urge for the development of new chemotherapeutic approaches. Cellular processes controlling biofilm formation and dispersion, such as quorum sensing systems and metabolic pathways, are important targets for the discovery of new bioactive compounds. 8-10The second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a key regulator of bacterial behavior, especially controlling the switch between the motile planktonic and sedentary biofilm-associated lifestyles. Cyclic di-GMP stimulates the biosynthesis of adhesins and exopolysaccharide matrix substances in biofilms and inhibits various forms of motility. In general, low intracellular c-di-GMP levels are associated with freeswimming cells, whereas bacter...

show abstract

“…Colonies were fixed with paraformaldehyde and stained with 0.05% crystal violet (Sigma). The number of colonies was analysed with Cell Profiler software 62 or absorbtion at 540 nm was determined after methanol extraction.…”

Section: High-throughput Screen Data Analysis and Hits Validation Amentioning

confidence: 99%

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

et al. 2011

View full text Add to dashboard Cite

TP53(tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140 ), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes.More than 30 years of intense research on the tumour suppressor gene TP53 has revealed its relevance in many aspects of tumour biology (reviewed in ref. 1). It is now well established that p53 (the protein product of TP53) activation leads to the execution of a complex genetic program that limits cellular proliferation and leads to senescence or apoptosis 2,3 . Several lines of evidence have pointed to an under-appreciated homeostasis function of p53 in normal, unstressed cells 4 . As a transcription factor, p53 can mediate the expression levels of its target genes, thereby adjusting cellular homeostasis of basic metabolism 5 , balance of reactive oxygen species 6,7 , stem cell identity and reprogramming 8 and animal reproduction 9 . These data establish an important role for p53 in cellular homeostasis and indicate that p53-loss-of-function cells become genetically rewired in a way that discriminates them from wild-type cells, a premise that could be explored for the identification of possible p53 genetic dependencies.Synthetic interaction screens have led the way in identifying new and unanticipated functional interactions between seemingly unrelated protein complexes in yeast 10,11 . In mammalian cells, RNA interference (RNAi)-based synthetic interaction screens are a promising approach to dissect genetic dependencies and the first studies on mammalian synthetic interactions of oncogenes have demonstrated the power of this approach 12,13 . Furthermore, synthetic lethal screens have identified genes that sensitize cells to different chemical drugs 14,15 . Several synthetic interactions with tumour suppressor genes have also been published 11,16 , but to our knowledge a genome-scale survey for synthetic interactions of a tumour suppressor gene has not been reported. Here, we present the results of a systematic investigation of TP53 genetic dependencies and characterize in molecular detail a homeostatic function of p53 in snoRNP biogen...

show abstract

CellProfiler™: Free, Versatile Software for Automated Biological Image Analysis

Cited by 822 publications

References 20 publications

Sex-lethal in neurons controls female body growth inDrosophila

Sex-lethal in neurons controls female body growth inDrosophila

Identification of Anti-Inflammatory and Anti-Hypertensive Drugs as Inhibitors of Bacterial Diguanylate Cyclases

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

Contact Info

Product

Resources

About