This unit presents detailed protocols for selection and propagation of landscape phages, which are fusions of filamentous phage fd (or its close relatives M13 and f1) and foreign DNA that result in chimeric phage virions with foreign peptides (8 to 9 amino acids long) covering the entire surface of the phage particles. These landscape phages bind specifically to mammalian and bacterial cells, spores, or discrete molecular targets.
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http://dx.doi.org/10.1002/0471140864.ps1809s51 | DOI Listing |
Unlabelled: Success of phage therapies is limited by bacterial defenses against phages. While a large variety of anti- phage defense mechanisms has been characterized, how expression of these systems is distributed across individual cells and how their combined activities translate into protection from phages has not been studied. Using bacterial single-cell RNA sequencing, we profiled the transcriptomes of ∼50,000 cells from cultures of a human pathobiont, infected with a lytic bacteriophage.
View Article and Find Full Text PDFChem Sci
December 2024
State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
Small ubiquitin-like modifier (SUMO) plays a pivotal role in diverse cellular processes and is implicated in diseases such as cancer and neurodegenerative disorders. However, large-scale identification of endogenous SUMO-1 faces challenges due to limited enrichment methods and its lower abundance compared to SUMO-2/3. Here we propose a novel combinatorial peptide strategy, combined with anti-adhesive polymer development, to enrich endogenous SUMO-1 modified peptides, revealing a comprehensive SUMOylation landscape.
View Article and Find Full Text PDFSci Total Environ
January 2025
CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
This study investigated the potential role of phages in the dissemination of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) in Escherichia coli (E. coli). A comprehensive in silico analysis of 18,410 phage sequences retrieved from the National Center for Biotechnology Information database (NCBI) revealed distinct carriage patterns for ARGs and VFGs between lytic, temperate, and chronic phage types.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
Genetically encoded libraries (GEL) are increasingly being used for the discovery of ligands for "undruggable" targets that cannot be addressed with small molecules. Foundational GEL platforms like phage-, yeast-, ribosome-, and mRNA-display have enabled the display of libraries composed of 20 natural amino acids (20AA). Unnatural amino acids (UAA) and chemical post-translational modification (cPTM) expanded GEL beyond the 20AA space to yield unnatural linear, cyclic, and bicyclic peptides.
View Article and Find Full Text PDFGut Microbes
December 2024
State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R China.
Prophages, which are an existing form of temperate phages that integrate into host genomes, have been found extensively present in diverse bacterial species. The human gut microbiome, characterized by its complexity, dynamism, and interconnectivity among multiple species, remains inadequately understood in terms of the global landscape of bacterial prophages. Here, we analyzed 43,942 human gut-derived bacterial genomes (439 species of 12 phyla) and identified 105,613 prophage regions in ~ 92% of them.
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