Journal: Nature Immunology

Article Title: Antigen specificity of clonally enriched CD8 + T cells in multiple sclerosis

doi: 10.1038/s41590-025-02412-3

Figure Lengend Snippet: a , Summary of EBV DNA ddPCR results from CSF supernatant in which EBER2 was normalized to a housekeeping gene (MS/CIS, n = 13; HC/OND, n = 5). b , EBV cDNA for each of the indicated genes were measured by ddPCR and normalized to a housekeeping gene. Each sample was run in duplicate and each dot represents the average result from each study participant. Data are the mean ± s.e.m. MS/CIS and HC/OND samples were compared using an unpaired two-tailed Student’s t -test with Welch’s correction; NS, not significant; n = 13 for MS/CIS for all genes except EBER2 where n = 12 due to lack of sufficient sample for MS27 and n = 5 in HC/OND for all genes except BamHI-W where n = 4 due to a lack of sufficient sample for OND4.

Article Snippet: Complementary DNA was synthesized using a ProtoScript first strand cDNA synthesis kit (NEB) using 6 μl RNA per 20 μl reaction volume according to the manufacturer’s instructions.

Techniques: Two Tailed Test

Journal: Clinical pharmacology and therapeutics

Article Title: Liquid Biopsy Enables Quantification of the Abundance and Interindividual Variability of Hepatic Enzymes and Transporters.

doi: 10.1002/cpt.2102

Figure Lengend Snippet: Figure 1 Multi-omic analysis of matched liver and plasma samples. (a) The experimental workflow started at collection of matched liver and blood samples from the same patients. Blood was fractionated to isolate plasma, followed by isolation of exosomes and extraction of cell-free RNA (cfRNA), which was analyzed by next generation sequencing (NGS). Tissue was homogenized and processed by differential centrifugation to extract membrane fractions, followed by proteolysis of membrane proteins and mass spectrometric analysis. (b) Exosomal pellets extracted from plasma by polymer-assisted precipitation were visually inspected and examined by transmission electron microscopy (×13,000). (c) The yields of cfRNA (from each sample) and corresponding reverse transcribed cDNA were assessed, which reflected variability between samples. (d) Sequencing quality was examined, reflecting high quality scores (Q-scores). (e) For tissue processing, the level of membrane recovery (mean ± SE of the mean) was assessed using resident markers of endoplasmic reticulum and plasma membranes. (f) Proteomic analysis by mass spectrometry generated peptide and protein data, reflecting consistently high numbers of identified peptides and on average similar numbers of proteins (mean ± SD). (g) Protein identification was carried out with a sufficient number of peptides per protein (mean ± SD). (h) Quantification of proteins was possible for 84% of identified proteins using global proteomic data (n = 2,143), spanning 5 orders of magnitude. Of these, targeted measurement of eight enzymes, four transferases, and four transporters was possible using signature peptide data relative to QconCAT standard; the rank order of key target proteins is shown.

Article Snippet: Reverse transcription was performed with 3.5 μl of isolated cfRNA using AmpliSeq cDNA Synthesis for Illumina (Cambridge, UK).

Techniques: Clinical Proteomics, Isolation, Extraction, Next-Generation Sequencing, Centrifugation, Membrane, Polymer, Transmission Assay, Electron Microscopy, Reverse Transcription, Sequencing, Mass Spectrometry, Generated