RNA is a central molecule of life which carries genetic information from DNA to make proteins. Some RNA molecules do not code for a protein but interact with other RNA molecules to alter their function. Specifically, RNA-RNA interactions are important in regulating protein synthesis in a timely manner during cell development and adaptation to changing environments. The discovery of such RNA-RNA interactions remains challenging. The research proposed here uses an innovative approach to identify all RNA-RNA interactions in bacteria. This method will allow us to study new modes of RNA-based regulation, and their regulatory role during bacterial infection.

A long-standing mystery in neuroscience is that many brain areas communicate with each other through multiple, parallel pathways. Is the same information delivered to multiple locations within one area? Alternatively, is different information delivered to different locations? Because parallel connectivity patterns are widely found in the brain, this feature presumably play a fundamental role in brain computations. This project will study such parallel pathways in the brain through combined use of state-of-the-art techniques and tiny optical tools I have recently developed. This new approach has potential to make a significant contribution to our understanding of the brain’s mysterious parallel communications.

Organisms interact with their surroundings through intricate signaling webs using chemical language. In this project, I will DECODE a hybrid chemical language jointly made by plants and their associated microbes but hijacked by parasitic nematodes. I will uncover how this language is created, who is listening to it, and what its fitness benefit is. I anticipate discovering an entirely new, important and evolutionary conserved, signaling molecule that is involved in the plant-beneficial microbe-nematode interaction.

Whitefly (Bemisia tabaci) infestations and subsequent transfer of viruses cause severe losses in crop production and horticultural practice. As a result of legislation demanding reduced pesticide usage, whitefly resistance has become of the most important breeding targets in vegetable crops, and we recently contributed to this for tomato (Solanum lycopersicum; PNAS, 2012). During the last years it has become clear that whiteflies can suppress some of the natural defenses of plants. Sap feeders like whiteflies and aphids secrete protein-rich saliva into leaf tissue. These salivary secretions contain so-called effectors that can manipulate plant defenses. For aphids several effectors have been characterized by expression in planta, which resulted in reduced aphid resistance. This project aims to identify effectors from whiteflies AND the plant proteins with which they interact. Putative effectors will be identified by analyses of transcriptomes of different whitefly biotypes combined with peptidomics and proteomics of saliva. This will give us candidate whitefly effectors, which we will validate via various transient plant assays and with stable transgenic plants. The two most potent effectors will be selected to find plant proteins with which they interact in tomato using yeast-2-hybrid and, if necessary, immunoprecipitation (IP) followed by mass-spectometry. Potential interactions will be confirmed by co-IP assays. Together these data will provide us the main plant proteins that whitefly effectors target to modulate induced defenses. Knowledge of these genes will facilitate breeding for increased whitefly resistance.