Very interesting study from Xiang X et al. about gRNA efficiency prediction, including a web based software CRISPRon for gRNA design (https://rth.dk/resources/crispr/crispron/).
Seraching for the perfect gRNA (Xiang X et al)!
Author: fredrikwermeling
BAR-Seq clonal tracking of gene-edited cells!
Beautiful work from Ferrari et al!
https://www.nature.com/articles/s41596-021-00529-x
Linked webpage for analysis:
Popular scientific texts and interviews
2018 / Text (Swedish) for the membership magazine Legatus Mensae (“A strong Immune System”):
2021 / Interview for CMM news (text by Magdalena Lindén) :
2021 / Interview for Nordic Life Science about the Nobel Prize in Chemistry for CRISPR (p. 38-43 here in English):
2020 / Interview for KI about the Nobel Prize in Chemistry for CRISPR (here in Swedish):
2020 / Interview for Reumatikervärlden, the membership magazine of the Swedish Rheumatism Association (in Swedish). Rumatikervärlden number 2 2020 page 36-37 (interview by Annika Sjöberg):
2005 / Text for the student magazine “Bukpressen”:
I was interview about the CRISPR Nobel prize!
New paper out by Sanjay!
Great work by Sanjay Boddul in the lab developing methods to study T cell receptors cloned from patients! The presented experimental pipeline enables rapid development of relevant humanized animal models for studying novel antigen-specific tolerance therapeutics.
Boddul SV, Sharma RK, Dubnovitsky A, Raposo B, Gerstner C, Shen Y, Iyer VS, Kasza Z, Kwok WW, Winkler AR, Klareskog L, Malmström V, Bettini M, Wermeling F.
In vitro and ex vivo functional characterization of human HLA-DRB1*04 restricted T cell receptors.
J Transl Autoimmun. 2021 March (Accepted). link
3000 free medical images
The Immune Epitope Database!
The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.
We have deposited our favorite CRISPR screen plasmid @Addgene
It’s a version of LentiGuide-puro where Sudeepta Panda and Long Jiang added P2A-eGFP after PuroR, lac-mRFP in the stuffer, and a cloning site directly after the sgRNA scaffold.
The plasmid allows for both puro and eGFP selection and MOI determination. The lac-mRFP in the stuffer gives a simple visual quality control step when expanding in bacteria (red=stuffer, white=spacer successfully introduced). The cloning site allows for introducing e.g. UMIs.
Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles
Beautiful paper from the Elling and Zuber Labs on a novel score to predict sgRNA efficiency. Also including a website for sgRNA design based on the VBC score: https://www.vbc-score.org/ . Brought to my attention by shared first author Julian Jude.
Paper: https://pubmed.ncbi.nlm.nih.gov/32514112/
Commentary: https://www.viennabiocenter.org/about/news/new-prediction-tool-sharpens-the-crispr-scissors/
I´ve made a new video about redundant and non-redundant genes in the CRISPR context
Traditional #CRISPR screens typically only identify genes that have a non-redundant role in the studied system. Still, these are likely good candidate drug targets.
The Wermeling lab at the Karolinska Institutet 