Maynooth University Faculty of Science & Engineering

Throughout Nature, organisms interact with each other. Some of these interactions may be mutualistic and benefit both partners whereas others may be parasitic and involve one organism benefiting to the detriment of the other. Research in my group (Applied Proteomics Laboratory) investigates such interactions, specifically those involving important plant, insect and microbial species of economic, biomedical and agricultural significance. We adopt an integrated approach employing genomics, transcriptomics and proteomics to identify and investigate the interactions at the molecular and cellular level. My work has elucidated the molecular basis of many interactions and is leading us to the development of practical strategies for pest management and insect conservation. I have considerable expertise in non-model organism proteomics and data analysis and routinely develop bespoke proteomic strategies for groups and collaborators applying proteomic methodologies to their research for the first time.

Competitive Science Foundation Ireland funding for Departmental quantitative mass spectrometry (MS) facilities was secured which has enabled multiple new projects within Biology at MU. This instrumentation is also available to external academic and industry users (Contact: caroline.a.batchelor@mu.ie).

All MS-related publications (67) to February 2020 are available at: https://www.maynoothuniversity.ie/sites/default/files/assets/document//Q%20Exactive%20Publications%20-20022020.pdf

Current research in our lab can be classified into four broad areas:

1. Aphid-plant interactions
A considerable component of our research involves the economically important plant pest, the aphid (the dreaded greenfy!). We are particularly interested in aphid-plant interactions and have developed methods to acquire and analyse aphid effectors (molecules that modulate or negate plant host defences) and saliva allowing us to identify the molecular determinants of plant resistance/susceptibility and aphid virulence/avirulence. This research which is conducted with numerous international collaborators is resulting in a more detailed understanding of the plant/aphid interaction and provides insight into host plant selection processes and the ongoing chemical arms race between plants and aphids that began 250 million years ago. I am a member of the International Aphid Genomics Consortium a group of over 120 International researchers responsible for sequencing and annotating the genomes of a number of aphid species including the recently published Acyrthosiphon pisum and coordinate the AphidAtlas project which involves the application of proteomic data to assist gene and genome annotation (proteogenomics). We are also interested in other aspects of aphid biology including symbiont interactions, immunology and reproduction.

2. Investigating the decline of a key ecological pollinator; the bumblebee
Bumblebees are key ecological service providers and play an essential role in the maintenance and productivity of both wild and commercial plant communities. However, these valuable pollinators are currently facing major declines due to a combination of factors including climate change, intensive agriculture, introduction of alien species, exposure to chemical toxins, and the spread of pathogens and parasites. Given their importance. little is known about the molecular level effects these factors have on bees and research in our group aims to address these knowledge gaps by characterising cellular and molecular level changes in bees to various stressors (pathogens, parasites and pesticides) in both native and commercial bees.We are also involved in a number of bumblebee conservation programmes and insect DNA barcoding studies and we have recently initiated the Bumblebee Nest Initiative on the Maynooth University campus in an attempt to provide nesting sites for emerging spring queens which will ultimately benefit the flora on campus with increased pollination services. I was a member of the Bumblebee Genome Initiative that published the genomes for Bombus terrestris and B. ignitus (see publications) and I was involved in immune gene and haemolymph protein annotation efforts.

3. Identification of natural bioadhesives with potential medical application
Many organisms have evolved highly adaptive mechanisms of adhesion that underpin crucial aspects of their habit. In collaboration with the UCD Nanofunctional Group we are investigating marine bioadhesive systems used by fish ectoparasites to attach to their slimy and wet host. We have sequenced the genome for one of these parasites and directly identified the protein components of the adhesive matrix using mass spectrometry based proteomics. These proteins are now being investigated further to determine their potential as synthetic bioadhesives.

4. Investigating the molecular basis of Ascariasis using a murine model
Ascariasis is a disease of humans caused by infection of the nematode Ascaris lumbricoides. It is very common in developing countries and it is estimated that over 800 million people are currently infected. In a collaborative effort with Professor Celia Holland (Trinity College Dublin) we apply quantitative proteomics to investigate host-parasite interactions between two murine strains with differential resistance to the nematode. Our work has uncovered clear intrinsic differences in the host liver proteome and the response to Ascaris which provides new insights into the molecular determinants of resistance. We plan to further expand this work in an attempt to identify novel molecular processes and targets for treating or even preventing this disease, one that affects almost one sixth of the human population.