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A blog by Ben Vezina
Running pairwise Single Nucleotide Variant analysis on a dataset of ~106k carbapenemase-positive genomes. Performed at the Department of Infectious Diseases, Monash University. Run using my tool: https://github.com/bananabenana/time_weighted_SNV_clusterer Expression of fluorescent protein CreiLOV in E. coli under five novel different Ligalactobacillus agilis La3 promoters I identified and constructed during my PhD. Performed at RMIT University for article: https://doi.org/10.1128/AEM.00392-21 A DNA gel on a UV-transilluminator prior to gel purification and cloning, performed at RMIT University. For article: https://doi.org/10.1128/AEM.00392-21 Streak plate of two clinical strains of Klebsiella pneumoniae. I used these in a large-scale analysis of K. pneumoniae metabolism. For article: https://doi.org/10.1371/journal.pbio.3003559 Ligalactobacillus agilis La3 transformed with recombinant vectors I constructed, allowing expression of fluorescent protein CreiLOV. Performed at RMIT University for article: https://doi.org/10.1128/AEM.00392-21 A cool pic of a bunsen burner flame. Lights out in the lab for this snap A multi-level network I made in Plotly to visualise the relationship between carbapenemase genes, plasmids and species. During my postdoctoral position at the Department of Infectious Diseases, Monash University My electronic lab notebook, using Obsidian. This is me downloading many genomes for outcomes for patients infected with Klebsiella pneumoniae. Inhibition of a Lactoplantibacillus isolate to mutants from the plantacyclin bacteriocin. For article: https://doi.org/10.1038/s41598-020-74332-1 Ethanol + dry ice (ethanol bath) to snap-freeze electrocompetent cells I made during my PhD at CSIRO. For article: https://doi.org/10.1128/AEM.00392-21 The DNAlluminati, a blue light trans-illuminator I custom built. This is used to visualise DNA without using UV, which can reduce cloning efficiency by damaging DNA Anaerobic jar used to grow anaerobic bacteria. A candle is used to deplete oxygen. I used to work a lot with Lactabacillus and Clostridial species Antibiotic concentration reference sheet I used during my PhD at CSIRO A plasmid map we made to assign a people to a bin roster at the Department of Microbiology, Monash University A Bradford protein assay I ran to do a semi-quantitative analysis of my purified protein, as we did not have an antibody. For article: https://doi.org/10.1038/s41598-020-74332-1 Cell counting I did after two-strain co-cultures to study K. pneumoniae metabolism. Performed at The Department of Infectious Diseases, Monash University. For article: https://doi.org/10.1371/journal.pbio.3003559 Washing a protein purification column. The spot plate method to quantify CFU/mL. Performed at The Department of Infectious Diseases, Monash University. For article: https://doi.org/10.1371/journal.pbio.3003559 Very early foray into bioinformatics and the command line during my PhD. Performed at RMIT University A look into the freezers at The Department of Infectious Diseases, Monash University Light microscopy after a Gram stain. Cannot remember the organism Light microscopy after a Gram stain. Cannot remember the organism A growth inhibition assay of Plantacyclin against indicator strains to quantify growth inhibition. For article: https://doi.org/10.1038/s41598-020-74332-1 My first lab bench at CSIRO! My third lab bench at RMIT University! My lab books from my first postdoc at Griffith University Machine learning code in my work on predicting outcomes for patients infected with Klebsiella pneumoniae Media making guide for bacterial growth media, at the Department of Microbiology, Monash University. During my PhD. Network layouts I was playing with, to fill any shape. A patch plate I am taking Ligalactobacillus agilis La3 transformants from, so I can bead-beat them in a 96-well plate to perform PCR. For article: https://doi.org/10.1128/AEM.00392-21 Patch plates of transformed Ligalactobacillus agilis La3, confirming successful double-crossover chromosomal mutagenesis via positive and negative resistance profiles. For article: https://doi.org/10.1128/AEM.00392-21 Addition of butanol to Lactoplantibacillus plantarum supernatant in step 1 of plantacyclin purification. Dropping funnels made my life easier. Performed at the Griffith Institute of Drug Discovery, Griffith University. For article: https://doi.org/10.1038/s41598-020-74332-1 How I access the MASSIVE high performance computing cluster visually, with Filezilla software Transwells with co-cultures of various lineages of Klebsiella pneumoniae at the Department of Infectious Diseases, Monash University. For article: https://doi.org/10.1371/journal.pbio.3003559 The first time I got a successful Western blot recombinant NetB from the chromosome of Ligalactobacillus agilis La3. A Western blot confirming the expression of recombinant NetB from the chromosome of Ligalactobacillus agilis La3 after 100 generations (n=3 colonies per passaging culture). For article: https://doi.org/10.1128/AEM.00392-21

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