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Immunity to malaria is often considered slow to develop but this only applies to defense mechanisms that function to eliminate parasites (resistance). In contrast, immunity to severe disease can be acquired quickly and without the need for improved pathogen control (tolerance). Using Plasmodium chabaudi, we show that a single malaria episode is sufficient to induce host adaptations that can minimise inflammation, prevent tissue damage and avert endothelium activation, a hallmark of severe disease. Importantly, monocytes are functionally reprogrammed to prevent their differentiation into inflammatory macrophages and instead promote mechanisms of stress tolerance to protect their niche. This alternative fate is not underpinned by epigenetic reprogramming of bone marrow progenitors but appears to be imprinted within the remodelled spleen. Crucially, all of these adaptations operate independently of pathogen load and limit the damage caused by malaria parasites in subsequent infections. Acquired immunity to malaria therefore prioritises host fitness over pathogen clearance.
Pubmed ID: 33752799
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Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsSoftware for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsAmerican chemical, life science and biotechnology company owned by Merck KGaA. Merger of Sigma Chemical Company and Aldrich Chemical Company. Provides organic and inorganic chemicals, building blocks, reagents, advanced materials and stable isotopes for chemical synthesis, medicinal chemistry and materials science, antibiotics, buffers, carbohydrates, enzymes, forensic tools, hematology and histology, nucleotides, proteins, peptides, amino acids and their derivatives.
View all literature mentionsA commercial protocol sharing tool, which allows scientists to check in protocols the way that computer scientists check in code.
View all literature mentionsSoftware package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
View all literature mentionsCloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.
View all literature mentionsSoftware for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsCommercial provider of equipment and resources for epigenetics research, biological sample preparation, and diagnostic assays. The products Diagenode provides include automation and semi-automation software, antibodies, reagents, kits, and shearing technologies.
View all literature mentionsAn Antibody supplier who also provides assay services and products.
View all literature mentionsThis monoclonal targets CD169
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets Nur77
View all literature mentionsThis monoclonal targets CD3epsilon
View all literature mentionsThis monoclonal targets I-Ab
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets CD45R (B220)
View all literature mentionsThis monoclonal targets NK-1.1
View all literature mentionsThis monoclonal targets CD16/32
View all literature mentionsThis monoclonal targets CD115
View all literature mentionsThis monoclonal targets Ly-6C
View all literature mentionsThis monoclonal targets CD27
View all literature mentionsThis monoclonal targets CD11b
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD16/CD32
View all literature mentionsThis monoclonal targets Ly-6A/E
View all literature mentionsThis monoclonal targets CX3CR1
View all literature mentionsThis polyclonal targets H3K4me1
View all literature mentionsThis monoclonal targets CD135 (Flt3)
View all literature mentionsThis monoclonal targets CD71
View all literature mentionsThis monoclonal targets F4/80
View all literature mentionsThis monoclonal targets TER-119
View all literature mentionsThis monoclonal targets Ly-6G
View all literature mentionsThis monoclonal targets CD34
View all literature mentionsThis monoclonal targets CD117 (c-Kit)
View all literature mentionsThis polyclonal targets H3K27ac
View all literature mentionsThis monoclonal targets CD106
View all literature mentionsThis polyclonal targets H3K9me3
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
View all literature mentionsUltrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsA Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
View all literature mentionsA high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
View all literature mentionsSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
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