Research line: Interactions and effects of nanomaterials and living matter

 

Because it is hard to get funded
for interdisciplinary work, in a domain
that does not regular publish in glossy
journals, I found my funding not with
national, but with the European
Commission.

As a multidisciplinary researcher I had to wait long to become an expert. Effectively, you have to be expert in more than one field. An, as I am experiencing right now, staying expert is a whole other dimension. Bit with a solid chemistry, computing science, cheminformatics, and chemometrics education, I found myself versatile that I at some point landed that grant proposal (the first few failed). Though, I have had my share of travel grants and Google Summer of Code projects (microfunding).

So, while I am trying to establish a research line in metabolomics (also with some microfunding) and one PhD candidate (own funding), my main research line is nanosafety. Because my background fits in well, and while data quality for predictive toxicology leaves to be desired, there is a lot of work we can do here, to make the most of what is being measured.

Indeed, there are many interesting biological, chemical, and chemo-/bioinformatics research questions here (just to name a few):

• does the mechanism of cell entry differ for different engineered nanomaterials?
• does it differ from how "natural" nanomaterials enter the cell?
• does the chemical composition of the nanomaterial change when it comes into contact with living matter? (yes, but how? is it stable?)
• how do we represent the life cycle of nanomaterials in a meaning full way?
• does each cell type respond in the same way to the same material? is this predominantly defined by the cell's epigenetics or by the chemical nature of the material?
• given the sparseness of physicochemical and biological characterization of nanomaterials, what is the most appropriate representation of a material: based on physicochemical description, ontological description, or chemical graph theory?
• can ontologies help us group data from different studies to give an over view of the whole process from molecular initiating event to adverse outcome?
• can these insights be used to reliably and transparently advice the European people about risk?

We try to define answers to these questions in a series of FP7/H2020 projects using an Open Science approach, allowing our analyses to be updated frequently when new data or new knowledge comes in. These are the funded projects for which I am (was) PI:

• eNanoMapper (EC FP7, ended, but since this project developed Open solutions, it is reused a lot)
• NanoCommons (EC H2020, our work focussing on continuing the common ontology)
• RiskGONE (EC H2020, focusing on reach regulatory advising based on scientific facts)
• NanoSolveIT (EC H2020, computational nanosafety)
• Sbd4Nano (EC H2020, disseminating nanosafety research to the EU industry)

In these projects (two PhD candidates, one postdoc), open science has been important to what we do. And while not all partners in all projects use Open Science approaches, what our groups does tries to be as Open as possible. Some open science projects involved:

• eNanoMapper Ontology (describe nanosafety knowledge/data)
• AMBIT ((nano)material database)
• WikiPathways (biological pathways)
• the Chemistry Development Kit (cheminformatics, nanoQSAR)
• OpenRiskNet (open computation; another project our group was involved in, developing many open solutions)
• Wikidata (spider in the Linked Open Data Cloude)
• Scholia (another project I am PI on, but about knowledge dissemination, not nano)
• BioSchemas (FAIR annotation of things)
• BridgeDb (identifier mapping)

If we want to read more about these projects in the scientific literature, check the websites which often have a page with publications and deliverables. Or check my Google Scholar profile. And for an overview of our group, see this page.