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06 Feb 2021
A new APP knock-in mouse has hit the scene. Researchers led by Pascal Sanchez, Denali Therapeutics, San Francisco, California, described the details in a paper posted to bioRxiv on January 20. They humanized the Aβ sequence in the mouse APP gene and knocked in three familial Alzheimer’s disease mutations: Swedish, Arctic, and Austrian. TREM2 expression and cytokine concentrations spiked in brain tissue, microglia flocked to plaques, neurites swelled, and tau and neurofilament light collected in their cerebrospinal fluid. Notably, microglia surrounding plaques seemed distressed the cells filled with lipids and revved up transcription of genes previously linked to a subset of microglia isolated from AD brain tissue. Denali, in collaboration with the Jackson Laboratory, will make this model open access for academics and companies alike.
18) and quality trimmed by using Trimmomatic version 0.36 (
19). Viral contigs were generated by using default settings with Vicuna version 1.1 (
20), and a de novo consensus assembly was generated by using Viral Finishing and Annotation Toolkit (V-FAT) version 1.1 (https://www.broadinstitute.org/viral-genomics/v-fat). Read data are available from the National Center for Biotechnology Information Read Archive (https://www.ncbi.nlm.nih.gov) under BioProject accession no. PRJNA661611.
Phylogenetic Reconstruction
21) and IQ-TREE version 1.6 (
22). We then constructed a maximum-likelihood phylogenetic tree with 1,000 ultrafast bootstrap replicates (
HCV Transmission Network Analyses
We uploaded Illumina paired-end reads to GHOST and subjected them to automatic quality control criteria. In brief, read pairs were filtered out if a read had 3 Ns (N indicates that software was not able to make a basecall for this base) or a length 185 bp. Each identifier on forward and reverse reads