commit 602ad326e98024f26d24b1f77bed180d9ccd120b Author: coolneng Date: Mon May 23 17:18:04 2022 +0200 Initial commit diff --git a/Notes.org b/Notes.org new file mode 100644 index 0000000..c41e8d5 --- /dev/null +++ b/Notes.org @@ -0,0 +1,24 @@ +#+TITLE: Notes +* Methods +** Whole genome sequencing -> PacBio, along with Illumina for error correction in 1% of contig bases +** Development of a new genome assembler, due to the large genome size (x10 human size) -> MARVEL +** Verification of the genome assembly using non-exonic ultraconserved elements (UCEs) and generation of a gene catalogue using mRNA to determine if these coded for conserved eukaryotic genes +** Previously developed molecular toolkit -> germline transgenesis, CRISPR gene mutation, viral transfection... -> Identification of the regeneration cells +* Findings +** The median intron size is quite large (12-17 times compared to humans) -> Smaller intron sizes in non-developmental genes, which could facilitate rapid transcription and upregulation +- Pax family of genes: + + | Presence | Absence | + | Pax10 | Pax7 | + | | Pax3 | + +Pax3 and its cis-regulatory elements seem to be absent due to a deletion, although experiments performed using CRISPR mutate the gene show that Pax7 performs the functions of Pax3 along with the usual Pax7 functions in axolotl + +** Limb regeneration +*** Use of published mRNA and miRNA transcripts and the authors' own transcriptional profiling -> identification of 5 upregulated transcripts +| Protein | Function | +| similar to tectorin | Extracellular matrix | +| Ly6 | uPAR surface receptor | +*** Mapping non-coding RNAs -> 93 pre-miRNA, 42 novel miRNAs +* Future work +Model organism to study the evolutionary basis of its regeneration ability diff --git a/bibliography/The axolotl genome and the evolution of key tissue formation regulators.pdf b/bibliography/The axolotl genome and the evolution of key tissue formation regulators.pdf new file mode 100644 index 0000000..d11048c Binary files /dev/null and b/bibliography/The axolotl genome and the evolution of key tissue formation regulators.pdf differ