Lmst

#Fungal infections are hard to treat due to #DrugResistance. @blake_billmyre &co use a high-throughput #TNseq system in #Cryptococcus neoformans to identify >1400 essential genes & reveal a role for #mitochondrial genes in #fluconazole sensitivity @PLOSBiology https://plos.io/4dz3iVm

Schematic of TN-seq in C. neoformans. Top left: Transposon insertions (orange arrow) into nonessential genes results in viable cells. In contrast, insertions into essential genes will result in dead and nonrecoverable cells. Top right: TN-seq works by generating a library of cells where each cell has a single independent transposon insertion in a random location. As in A, those insertions into essential regions cause the cells to die and are nonrecoverable. As a result, the total library (bottom) is depleted in insertions in essential regions. Bottom: The Ac/Ds transposon was split into an Ac transposase and a Ds transposon containing a neomycin resistance marker. This Ds transposon was integrated into an intron of URA5 and the Ac transposase was integrated into the safe haven locus. The resulting stain is ura− and neomycin resistant. Upon initiating transposition via growth on galactose, the strain becomes URA+ and mutant at another locus (depicted here as YFG1).

A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks | Molecular Systems Biology
#tnseq
https://www.embopress.org/doi/full/10.15252/msb.202211398

#Genome-wide screen in human plasma identifies multifaceted complement evasion of #Pseudomonas aeruginosa | PLOS #Pathogens
#tnseq

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011023

Quantifying the local #adaptive landscape of a nascent bacterial community

#tnseq #evolutionarypaths
https://www.nature.com/articles/s41467-022-35677-5

Revealing Causes for False-Positive and False-Negative Calling of Gene #Essentiality in Escherichia coli Using #Transposon Insertion Sequencing

#tnseq #functionalgenomics

https://journals.asm.org/doi/10.1128/msystems.00896-22

This useful paper looks into strengths and weaknesses of #TnSeq approaches in #bacterial #genetics screens for essential genes.

Importantly, a lot of false positives are attributable to Tn insertion failure on nucleoid-associated DNA — a result that my friends who use #ATACSeq & similar methods to map chromatin states in eukaryotes will be unsurprised by.

The obvious workaround is in vitro transposition on isolated DNA, if your system is amenable to that approach.

https://journals.asm.org/doi/full/10.1128/msystems.00896-22

Construction of high-density #transposon mutant library of Staphylococcus aureus using #bacteriophage ϕ11 -
#tnseq

https://pubmed.ncbi.nlm.nih.gov/36422842/

So, I'm checking whether a transposon from a TB library for Tn-Seq experiments is actually present in the sequenced genome. #bioinformatics #microbiology #tuberculosis #tnseq Can I just try to align the transposon sequence to the contigs to see if its present? PCR failed to find the transposon in the isolate, so I should expect that the transposon sequence won't align to the contigs of the genome?

#TNseq

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