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Immunology

Best bioinformatics software for mass-cytometry analysis

Conventional flow cytometry is limited by the number of fluorochromes and cell markers that can be targeted at once. Overcoming this limitation, mass-cytometry combines mass-spectrometry and flow cytometry by using metal-conjugated antibodies to label cellular proteins and extend the number of markers to be targeted.   A combination of spectrometry and cytometry   In mass-cytometry, antibodies are conjugated with isotopically pure elements, and these antibodies are used to label cellular proteins. Cells are nebulized and sent through an argonplasma, which ionizes the metal-conjugated antibodies. The metal signals are then analyzed by a time-of-flight mass spectrometer. The approach overcomes limitations of spectral overlap in flow cytometry by utilizing discrete isotopes as a reporter system instead of traditional fluorophores which have broad emission spectra.   Due to its numerous advantages (minimal …

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Best bioinformatics software for single-cell RNA sequencing

RNA-sequencing is often performed on well-identified groups of cells thought to be homogeneous. However, quantification of molecular changes is made by estimating the mean value from millions of cells and averaging the signal of individual cells, thus ignoring cell-to-cell heterogeneity. Single-cell RNA-sequencing (scRNAseq) enables to unravel the heterogeneity of cell genotype, phenotype, and function within a given subpopulation.   ScRNA-seq now has a wide variety of applications, and numerous tools were developed to analyze this new kind of sequencing data. To help you perform your experiments in the best conditions, we asked OMICtools members to choose their favorite scRNA-seq analysis tools.   Main applications for scRNA-sequencing   Single-cell RNA sequencing finds its main applications in immunology, cancerology, and the study …

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Simulate immune responses to vaccines with C-IMMSIM

Because of the diversity of the immune repertoires, it is very challenging to predict the efficacy of a vaccine to properly stimulate all components of the immune system and ultimately protect against infectious diseases, that is it’s immunogenicity. To aid researchers in the design and set up of their vaccination/infection protocols, Dr. Filippo Castiglione and colleagues from the Institute for Applied Computing in Rome have developed C-IMMSIM. Here, he talks about the features and benefits of his tool. A novel and free tool to perform in silico experiments about vaccinations and/or infections To date, this is the only simulation tool for the immune response which combines epitope/peptide prediction algorithms with agent-based methodology to predict the follow-up of virtual infection experiments. …

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Single-cell RNA sequencing in immunology

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the immune system and now has a wide range of applications in immunology. This technology spans the whole genome and provides an unbiased gene expression profile of individual cells. Bulk vs single-cell RNA-seq Traditional bulk RNA-seq is often performed on well-identified groups of cells thought to be homogeneous. However, quantification of molecular changes is made by estimating the mean value from millions of cells and averaging the signal of individual cells, thus ignoring cell-to-cell heterogeneity, which is a hallmark of adaptive immune cell subsets such as B and T lymphocytes. The need to identify new and discrete immune cell populations and to understand molecular changes that occur at the single cell level …

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