Phi-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays

International audiencePhenotypic screening monitors phenotypic changes induced by perturbations, including those generated by drugs or RNA interference. Currently-used methods for scoring screen hits have proven to be problematic, particularly when applied to physiologically relevant conditions such as low cell numbers or inefficient transfection. Here, we describe the Phi-score, which is a novel scoring method for the identification of phenotypic modifiers or hits in cell-based screens. Phi-score performance was assessed with simulations, a validation experiment and its application to gene identification in a large-scale RNAi screen. Using robust statistics and a variance model, we demonstrated that the Phi-score showed better sensitivity, selectivity and reproducibility compared to classical approaches. The improved performance of the Phi-score paves the way for cell-based screening of primary cells, which are often difficult to obtain from patients in sufficient numbers. We also describe a dedicated merging procedure to pool scores from small interfering RNAs targeting the same gene so as to provide improved visualization and hit selection

Resilience in a cheese ecosystem

Resilience in a cheese ecosystem. 14. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 201

Combining kinetic modeling and transcriptomic analysis to study the resilience 2014 on a model of microbial ecosystem

Combining kinetic modeling and transcriptomic analysis to study the resilience 2014 on a model of microbial ecosystem. ECCB'14 : European Conference on Computational Biolog

Chemo-enzymatic synthesis of glycolipids, their polymerization and self-assembly

This paper describes the synthesis of bio-based methacrylated 12-hydroxystearate glucose (MASG), and its (co)polymerization with methyl methacrylate (MMA) by either free-or RAFT radical polymerizations. The obtained amphiphilic p(MMA-MASG) copolymers self-assembled in water into various morphologies depending on the MASG unit content and glycopolymer crystallinity. Finally, as a proof of concept, a hydrophobic dye, Nile Red, was entrapped by co-nanoprecipitation into p(MMA-MASG) nanoparticles, showing their loading capacity and thus demonstrating the potential of such amphiphilic glycolipid-based copolymers in hydrophobic compound encapsulation applications

Microstructure evolution and deformation mechanisms during compression of a harmonic–structured Ti–24Nb–4Zr–8Sn alloy

Processing heterogeneous microstructures, especially the so-called harmonic structures consisting of soft core and hard shell regions, is an efficient way to achieve a strength-ductility trade-off in classical metallurgy. In this study, two harmonic samples with the same composition of Ti–24Nb–4Zr–8Sn but different microstructures were processed to exhibit different grain size heterogeneities between the core and the shell. Both samples were consolidated from a ball-milled powder using Spark Plasma Sintering (SPS) but applying two different sintering times, 1 and 60 min. The grain size heterogeneities were higher for the longer SPS sintering time due to the enhanced grain dimension in the core for 60 min consolidation time. The mechanical behavior of the two materials was studied via a monotonic quasi-static compression test. For both harmonic-structured Ti–24Nb–4Zr–8Sn alloys, a high compressive proof stress of about 1 GPa was detected. The strain-hardening rate was higher for the longer SPS time due to the higher grain size differences between the core and shell. A high dislocation density was detected in both materials after compression deformation (several tens of 1014 m−2). The dislocations tend to form cells and LAGBs during compression. The dislocation pile-ups at the core-shell interfaces caused a back stress of about 640 MPa after compression at 2–5% strains. The contributions of the different features of the microstructure (grain size, α phase precipitates, and oxygen concentration) to the proof stress were determined

Overview of a surface-ripened cheese community functioning by meta-omics analyses

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process

Sequencing coverage (C) and percentage of genes (P) with at least an average of five uniquely mapped reads in the DNA-Seq dataset across the three replicates for each microbial genome during ripening.

<p>^aAA = <i>Arthrobacter arilaitensis</i>; BA = <i>Brevibacterium aurantiacum</i>; CC = <i>Corynebacterium casei</i>; DH = <i>Debaryomyces hansenii</i>; GC = <i>Geotrichum candidum</i>; HA = <i>Hafnia alvei</i>; KL = <i>Kluyveromyces lactis</i>; LL = <i>Lactococcus lactis</i>; SE = <i>Staphylococcus equorum</i></p><p>Sequencing coverage (C) and percentage of genes (P) with at least an average of five uniquely mapped reads in the DNA-Seq dataset across the three replicates for each microbial genome during ripening.</p