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This chapter describes optimized RNA-seq workflows for studying PNA-CPPs in Escherichia coli and Salmonella enterica; discusses considerations for RNA isolation, sequencing strategies, and data analysis; and emphasizes the importance of robust, reproducible pipelines for reliable data interpretation.
This protocol enables effective cell lysis, nucleic acid purification, and efficient removal of genomic DNA while preserving all transcript classes, including small regulatory RNAs (sRNAs), and provides a basis for future studies investigating the gene expression dynamics and regulatory networks of F. nucleatum under d...
Macrophages are essential for both, to clear pathogens and preserve tissue homeostasis, yet the molecular regulators of this equilibrium remain incompletely defined. Here, we identify SAILR (survival associated immune-regulatory RNA), a primate-specific long noncoding RNA (lncRNA), as a critical modulator of macrophage...
Abstract Neisseria meningitidis is a human-adapted commensal pathogen that must continuously balance nutrient acquisition with stress tolerance. Here, we identify a type II-C CRISPR/Cas-associated small RNA (scaRNA) as a posttranscriptional regulator of the efeUOB operon and oxidative stress responses. Using in vitro R...
Findings indicate that the specific identity of the CPP used plays a key role in determining its robustness against the evolution of resistance, and that laboratory evolution can illuminate the remaining gaps in the authors' knowledge on the mechanisms of action of asobiotics.
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