I'm a systems & synthetic biologist by training and recently completed my PhD in the Department of Biology at ETH Zurich. I'm interested in studying how complex biological systems work and interact and want to try and apply this knowledge to solve global problems using new biotechnology. My experimental systems biology research approach employs CRISPR-based gene editing, long-read DNA/RNA sequencing, quantitative protein mass-spectrometry, and targeted protein biochemistry.
Currently, I am studying the mechanisms by which plants (and other eukaryotes) produce complexity while having a limited set of genes. These “post-genetic” mechanisms (RNA splicing, protein phosphorylation and extra-chromosomal circular DNAs) are expansions of the classical Central Dogma, and my research suggests they’re an important part of how plants adapt to changing environments.
Linking CRISPR-Cas9 interference in cassava to the evolution of editing resistant geminiviruses
Genome Biology (2018)
Here we tried to use CRISPR-Cas9 technology to engineer resistance to DNA viruses in cassava. We used CRISPR-Cas9 encoded by the plant to cleave the DNA of replicating viruses. However, we found that by 8 weeks after inoculation by the virus, a stable, new mutant virus evolved, which was resistant to further cleavage by the Cas9-sgRNA system. Our results point to a novel environmental containment consideration for regulating the release of plants constitutively expressing Cas9 and sgRNAs targeting a virus.
A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field
Nucleic Acids Research (2019)
In this paper I present a new method for deep-sequencing viruses accurately. This new method can enrich circular DNA from a background of linear DNA, and then sequence circular DNA using a long-read sequencing method. Essentially this means we can, for the first time ever, obtain full-length virus genomes from single-molecule sequencing reads. Our method called CIDER-Seq is also 16x cheaper than conventional approaches and can even be used to sequence viruses with no prior sequence information. We applied CIDER-Seq to samples collected from a confined field trial of transgenic virus-resistant cassava plants and discovered the extent to which anti-viral RNAi technology can affect wild virus populations.
Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch
Science Advances (2018)
Here my colleagues and I invented a new application of CRISPR-Cas9 technology for crop plants that are difficult to breed by conventional means. We combined CRISPR with a gene that causes the induction of flowering. We used this to produce genome-edited cassava plants that produced a new, industry-preferred type of starch in their roots. Since these plants were engineered to flower early, we could then cross the plants to eliminate any trace of transgenesis in the plant’s offspring. Thus the system allowed us to rapidly breed genome-edited cassava plants that have a ready industrial application and could be commoditized by small-holder farmers in the Global South.
Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes
BMC Genomics (2017)
Protein acetylation is an important chemical modification present on many proteins in all eukaryotes. Here we analysed the enzyme families that catalyse the acetylation of proteins in 53 different species in the plant lineage. Our analysis covered gene counts, protein domain conservation, phylogenetic relationships, expression patterns and promoter elements for each gene family. This study thus serves as a compendium of useful information about this key regulatory process which can be used for more targeted studies into protein acetylation in photosynthetic eukaryotes.
Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response
Molecular Plant Pathology (2017)
In this study we studied the expression of every gene in two cassava varieties (one resistant, and one susceptible) upon infection with the Cassava brown streak virus. Our results allowed us to make conclusions regarding the various mechanisms employed by cassava to fight virus infection. We also compared our dataset against gene-expression data from other plants to identify common genes involved in fighting off virus infection among diverse plant species.
Characterization of Brown Streak Virus–Resistant Cassava
Molecular-Plant Microbe Interactions (2016)
Here we identified an elite cassava breeding line which is completely resistant to the devastating Cassava brown streak virus. We demonstrated that the plant can resist infection by two species of this virus. We used a really cool double-grafting approach to show that, though resistant to infection, the variety still allowed the virus to move through its vasculature. We used a protoplast assay to show that the resistant variety also limited the replication of the virus intra-cellularly.