Promoters play a key role in influencing transcriptional regulation for fine-tuning the expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated, but few have attempted to develop theoretical methods to predict the strength of promoters from their nucleotide sequence. Such theoretical methods are not only valuable in the design of promoters with specified strength but are also meaningful in understanding the mechanistic role of promoters in transcriptional regulation. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence in Saccharomyces cerevisiae . We infer from our analysis that the −49–10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict promoter strength. https://qpromoters.com/ and a standalone tool https://github.com/DevangLiya/QPromoters to quickly quantify the strength of Saccharomyces cerevisiae promoters.

Promoters play a key role in influencing transcriptional regulation for fine-tuning expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated but few have attempted to develop theoretical methods to predict the strength of promoters from its nucleotide sequence.Such theoretical methods are not only valuable in the design of promoters with specified strength, but are also meaningful to understand the mechanism of promoters in gene transcription. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence in Saccharomyces cerevisiae. We infer from our analysis that the −49 to 10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict the promoter strength. We present an online tool https://qpromoters.com/ that takes advantage of this fact to quickly quantify the strength of the promoters.

CD8+ T lymphocytes play vital roles in killing infected or deranged host cells, recruiting innate immune cells, and regulating other aspects of immune responses. Like any other cell, CD8+ T cells also produce extracellular particles. These include extracellular vesicles (EVs) and non‐vesicular extracellular particles (NVEPs). T cell‐derived EVs are proposed to mediate cell‐to‐cell signalling, especially in the context of inflammatory responses, autoimmunity, and infectious diseases. CD8+ T cells also produce supramolecular attack particles (SMAPs), which are in the same size range as EVs and mediate a component of T cell mediated killing. The isolation technique selected will have a profound effect on yield, purity, biochemical properties and function of T cell‐derived particles; making it important to directly compare different approaches. In this study, we compared commonly used techniques (membrane spin filtration, ultracentrifugation, or size exclusion liquid chromatography) to isolate particles from activated human CD8+ T cells and validated our results by single‐particle methods, including nanoparticle tracking analysis, flow cytometry, electron microscopy and super‐resolution microscopy of the purified sample as well as bulk proteomics and lipidomics analyses to evaluate the quality and nature of enriched T cell‐derived particles. Our results show that there is a trade‐off between the yield and the quality of T cell‐derived particles. Furthermore, the protein and lipid composition of the particles is dramatically impacted by the isolation technique applied. We conclude that from the techniques evaluated, size exclusion liquid chromatography offers the highest quality of T cell derived EVs and SMAPs with acceptable yields for compositional and functional studies.

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The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome has shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike sub regions and have observed that the different variants harbour unique signature patterns in the spike sub regions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions.