Optimisation of methods for genome sequencing SARS-CoV2 genomes (virus causes COVID-19)
Supervisor(s): Dr Nikki Freed
Supervisor’s webpage: https://sites.google.com/view/thefreedlab/home
Project Description
Our lab has recently developed a method to sequence the genome SARS-CoV2, the virus that causes COVID-19. This method is being used internationally and has worked well. However, we would like to fine tune it to further reduce costs and the ability to sequence the entire genome even when there are just a few copies of the virus present. This work will be done in a PC2 lab, but you will be working with non-infectious synthetic RNA to mimic the real virus. You will compare the effect of using different polymerases and protocols using nanopore DNA sequencing. This work requires exceptional laboratory notebook skills, careful attention to detail, the ability to think critically about results, and be able to work independently when required.
Pathogen profiling using CRISPR-Cas9 and next generation sequencing
Supervisor(s): Dr Olin Silander
Supervisor’s webpage: https://www.silanderlab.com/news
Project Description
Rapid determination of pathogen strain type and antibiotic resistance profile is critical for reducing patient mortality. In this project the student will work to improve the efficiency of a novel method we have developed for pathogen strain typing and antibiotic resistance profiling. This method is based on CRISPR-cas9 targeting and enrichment of specific pathogen DNA sequences, followed by real time sequencing on the Oxford Nanopore MinION next generation sequencing platform. This project will provide a real opportunity for the student to meaningfully contribute to scientific research while enabling the student to learn cutting edge molecular biology and genomic sequencing techniques.
Selection of antibiotic resistance: do different paths lead to different outcomes?
Supervisor(s): Professor Tim Cooper
Supervisor’s webpage: http://cooperlab.org/people
Project Description
Bacterial resistance to antibiotics is a major concern for the treatment of bacterial disease. Understanding consequences of resistance is necessary to allow best use of current antibiotics and to predict how resistance to specific antibiotics will impact resistance to others. We will examine a specific question: how does the evolutionary path a population takes to acquire a resistance profile affect other attributes of that population? For example, does evolving resistance to a particular antibiotic first, rather than second, along an evolutionary path, make it more or less likely that a population can evolve another resistance? Resistance affects many characteristics of cells, so these kinds of dependencies are easy to imagine and may even be unavoidable. To address this question, we will track changes in a population of initially sensitive bacteria that is divided into sub-populations and selected to evolve resistance to three antibiotics in each of the six possible combinations.
Assessing the effects of copper on biofilm formation by Psa, a pathogenic bacterium of kiwifruit
Supervisor(s): Associate Professor Xue-Xian Zhang
Supervisor’s webpage: https://sites.google.com/view/xxzhang/home
Project Description
Copper spraying is among the most effective practices in managing Pseudomonas syringae pv. actinidiae (Psa) infection of kiwifruit orchards in New Zealand, but its effectiveness is threatened by the emergence of copper-resistant (CuR) Psa strains. Much attention has been focused on the detection of CuR strains and underlying resistance genes. There remains a significant gap in our understanding of how the copper-based bactericides work once they are applied to plants. More specifically, the bioavailability of Cu2+ and their efficacy in controlling Psa growth and lesion development have not been examined in the plant environment. In this summer project, the newly developed bacterial biosensors will be used to assess the effects of copper on a specific type of bacterial growth, i.e. biofilm formation on abiotic and biotic surfaces. The data will help determine how much copper is required to control Psa.
Recapitulation of Genes Involved in Cheating Behaviours in Dictyostelium discoideum
Supervisor(s): Dr Elizabeth Ostrowski
Supervisor’s webpage: http://ostrowski-lab.org/
Project Description
Dictyostelium discoideum, the social amoeba, is a model system for cooperation and conflict. When starved, the single-celled amoebae communicate, aggregate, and differentiate to form a multicellular fruiting body. Approximately 20% of cells sacrifice their lives to form the stalk of the fruiting body, while the remainder survive as spores. Because genetically different strains can co-aggregate and form fruiting bodies together, there is potential for conflict over which strains will die and form the stalk and which will live. Previously we used insertion mutants that “cheat” (i.e., preferentially form spores) to select for “resistant” strains, which show improvements in equitable spore production when co-developed. The student will re-capitulate a cheater mutation into the genetic background of wild-type cells in order to ascertain its effect on cheating, apart from other changes in the genome. This work will involve plasmid rescue from the mutant followed by transformation of wild-type cells.
Bacteriophages for defending honeybees against a bacterial pathogen
Supervisor(s): Dr Heather Hendrickson
Supervisor’s webpage: http://abate.massey.ac.nz/
Project Description
Bacteriophages are the viruses of bacteria and these tiny entities have been demonstrated to protect beehives abroad that are threatened by a bacterial pathogen (Paenibacillus larvae). We have isolated 34 native P. larvae bacteriophages in New Zealand and we are in the process of
- Studying their ability to infect the diverse pathogens we find here
- Studying the degree of antibiotic resistance found in these pathogens in New Zealand
- Working to identify an alternate host strain that we can use in a citizen science phage hunt for these fascinating bacteriophages and
- Testing the ability of these bacteriophages to infect the spore form of this pathogen
There are many elements of this project that a student could pursue over the summer and we would love to see you give us a hand in the Hendrickson lab on an aspect of this project that interests you.