Congrats to Markéta, who passed her PhD examination with no emendations (something achieved by only 5% of all students)!!
Bhargava spoke at the 2021 FAOBMB meeting on detecting RNA modifications in bacteria using Oxford Nanopore sequencing.
New preprint from Georgia - Do You Want to Build a Genome? Benchmarking Hybrid Bacterial Genome Assembly Methods, in which we work towards ranking assembly methods using a number of different metrics.
New preprint: Gene regulation is commonly selected for high plasticity and low noise. We show that in E. coli, selection acts strongly to increase plasticity - the difference in expression level of a gene in one environment versus another. A huge effort by Markéta.
We've posted a new pre-print in which we explore whether a self-splicing ribozyme (RiboJ) behaves robustly across different cis- and trans- genetic contexts. Congrats to Markéta, who did the vast majority of work on the project!
We have a two-year fully funded MSc Scholarship (with stipend) available, starting as soon as possible. The project will examine interactions between bacteria and whether these interactions change if bacteria have different environmental histories (and memories of those different histories). Please email if this sounds interesting! There is some flexibility in the direction that the project takes.
(Ex lab-associate) William Pearman's paper Concordant geographic and genetic structure revealed by genotyping‐by‐sequencing in a New Zealand marine isopod (modified title from the pre-print here) is published in Ecology and Evolution!
New Marsden grant! Predicting evolution: Quantifying the emergence of antibiotic resistance in diverse environmental strains of E. coli, $300K. Nikki Freed (PI) and Olin Silander (AI)
Congrats to Julia White, who was awarded one of the $3K SNCS Summer Scholarships (again!)!
New preprint out: The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand. We played a small part in getting the sequencing data for this study, which was led by Jemma Geoghegan
Andrea's manuscript on profiling bacterial strains and antimicrobial resistance loci using CRISPR-Cas9 enrichment and long read sequencing (Bac-PULCE) is now posted as a preprint on bioRxiv!
Congratulations to Georgia Breckell and Markéta Vlková, who were both awarded Sir Neil Waters Scholarships
Olin, Nikki, and Markéta completed genome sequencing for 19 new SARS-CoV-2 genomes (in ~ 8 hours for each set of samples) to establish linkages for the new SARS-CoV-2 outbreak in Auckland. News story here. Link to some Twitter discussions and here (with article) and here. This was very exciting work and provided the first genomic evidence that this was a single cluster.
One day later William Pearman has left the building to start his PhD at Otago :( Good luck!
Welcome to Stella Pearless, a new MSc who will work on characterising phenotype switching in natural isolates of E. coli!
Congrats to Bhargava for passing his PhD confirmation!
Sara Burgess from Massey Palmerston North is up for the week to improve her Oxford Nanopore sequencing technique (PhCHCl3 and circulomics) and get in some data analysis. Hopefully we won't disappoint her with mediocre run yields.
Markéta (Effects of Single SNPS on Gene Expression) and Georgia (So you wanna build a genome) presented talks at the New Zealand Microbiological Society 2019 meeting, while Georgia, Andrea (Rapid CRISPR-based Identification of Microorganisms - a Proof of Concept), Bhargava (Full length cDNA sequencing to study transcriptional regulation in bacteria), and Alyssa (Metagenomic analysis of cow faecal samples) presented posters.
We've started a collaboration with Fonterra to profile the community of their membrane bioreactors using metagenomic and 16S analyses. More faeces!
A brilliant month of rejections: Andrea (PhD scholarship application rejected); Olin (AMRF grant rejected); and fellow PI Nikki Freed (2nd round Marsden grant rejected). Moving on...
Congrats to William and Bhargava for their awards at the annual SNCS postgraduate conference (1st place talk and 2nd place poster presentation, respectively).
Congrats to Julia White, who was awarded one of the $6K SNCS Summer Scholarships!
Welcome to Julia White, who is joining the lab as an undergraduate volunteer.
Olin gave one of the monthly seminars organised as part of the Evolution Research @ Auckland Network.
Welcome to Jamie le Roux, who is joining the lab as a Research intern.
Welcome to Andrea Sajuthi, who is joining the lab as a new PhD student.
Welcome to Katie Littlewood, who is joining the lab as an undergraduate intern.
We were awarded $10K in seed funding from the Digital Life Institute for proof-of-concept design and production of synthetic bacteriophage.