Nature research paper: A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage
, MA plots of the median expression ratio between infected and uninfected hepatocytes, split into 10 spatio-temporal bins. Y axis indicates log2 of the median ratio per gene. X axis indicates log10 of the gene’s max average expression. Genes significantly increased or decreased in infected hepatocytes are plotted in red or blue respectively . The names of selected genes from Fig., Gene set enrichment analysis for highly expressed genes ranked based on ratio changes indicated in .
Red blow up of 100x100 pixels around a pericentral infected cell. Letters indicate the infected cells plotted on, Histogram of median pixel value of random neighborhoods in the image shown in , red X represent values of infected neighborhoods labeled correspondingly to the yellow labels in . Note that infected cell ‘C’ resides in a more periportal zone ., smFISH quantification demonstrates lower proportions of infected periportal hepatocytes at 40hpi.
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Probing the dynamic RNA structurome and its functions - Nature Reviews GeneticsIn this Review, Spitale and Incarnato discuss how the application of sequencing-based RNA structure mapping methods to entire transcriptomes in living cells is providing insight into the RNA structurome, the dynamics of RNA ensembles and how RNA structure regulates cellular processes.
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Frontiers | The epitranscriptome of Vero cells infected with SARS-CoV-2 assessed by direct RNA sequencing reveals m6A pattern changes and DRACH motif biases in viral and cellular RNAsThe epitranscriptomics of the SARS-CoV-2 infected cell reveals its response to viral replication. Among various types of RNA nucleotide modifications, the m6A is the most common and is involved in several crucial processes of RNA intracellular location, maturation, half-life and translatability. This epitranscriptome contains a mixture of viral RNAs and cellular transcripts. In a previous study we presented the analysis of the SARS-CoV-2 RNA m6A methylation based on direct RNA sequencing and characterized DRACH motif mutations in different viral lineages. Here we present the analysis of the m6A transcript methylation of Vero cells (derived from African Green Monkeys) and Calu-3 cells (human) upon infection by SARS-CoV-2 using direct RNA sequencing data. Analysis of these data by nonparametric statistics and two computational methods (m6anet and EpiNano) show that m6A levels are higher in RNAs of infected cells. Functional enrichment analysis reveals increased m6A methylation of transcripts involved in translation, peptide and amine metabolism. This analysis allowed the identification of differentially methylated transcripts and m6A unique sites in the infected cell transcripts. Results here presented indicate that the cell response to viral infection not only changes the levels of mRNAs, as previously shown, but also its epitranscriptional pattern. Also, transcriptome-wide analysis shows strong nucleotide biases in DRACH motifs of cellular transcripts, both in Vero and Calu-3 cells, which use the signature GGACU whereas in viral RNAs the signature is GAACU. We hypothesize that the differences of DRACH motif biases, might force the convergent evolution of the viral genome resulting in better adaptation to target sequence preferences of writer, reader and eraser enzymes. To our knowledge, this is the first report on m6A epitranscriptome of the SARS-CoV-2 infected Vero cells by direct RNA sequencing, which is the sensu stricto RNA-seq.
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Observation of a new type of self-generated current in magnetized plasmas - Nature CommunicationsFusion devices like tokamaks require plasma current to generate magnetic field for plasma confinement. Here the authors report an observation of a self-generated anomalous current that contributes up to 30% of the total current in the fusion plasma at KSTAR.
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Condensation and thermalization of an easy-plane ferromagnet in a spinor Bose gas - Nature PhysicsA quantum simulation experiment reveals the thermalization of a ferromagnetic system realized with a one-dimensional spinor Bose gas, providing quantitative insights into the condensation dynamics of large magnetic systems.
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Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir - NatureNature research paper: Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir
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A new treaty process offers hope to end plastic pollution - Nature Reviews Earth & EnvironmentThe development of a global legally binding treaty by the UN to end plastic pollution is underway. To be effective, the global treaty requires new levels of transparency, disclosure and cooperation to support evidence-based policymaking that avoids the fragmented and reactionary policies of the past.
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