Department of Toxicogenomics

BE BASIC Biobased solutions for a sustainable society

finalized

16:43:44BE-Basic is an international public-private partnership between the Dutch government, world class universities, research institutes and advanced industries of various scales in the field of sustainable chemistry and ecology. The mission is to develop industrial biobased solutions for a sustainable society. BE-Basic supports the development of clean, robust and competitive biobased chemicals, materials and energy industries, including responsible monitoring and control of healthy soil and water environments, on the basis of advanced genomics technologies and bioprocess engineering. BE-Basic unifies the capabilities of Dutch and international worldclass universities, institutes and advanced industries of various scales.

Research within BE-Basic is organized across industrial collaborations on the one hand and fundamentally scientific projects on the other hand: the so-called Flagships bring together scientific topics and industrial challenges with the aim of generating true innovations. They represent the areas in which B-Basic as a whole, integrated with Ecogenomics, distinguishes itself and will ensure outstanding results on an international level. Nine Flagships are defined, each addressing a major scientific/socio-economic challenge:

  1. Carbon-based compounds
    aims to develop clean, efficient and otherwise sustainable industrial processes for carbon-based chemical building blocks mainly for the chemicals, materials and fuels industries. (Dr. Hein Stam, DSM; Prof. dr. Gerrit Eggink, Wageningen UR)
  2. Nitrogen-based specialties
    aims to develop novel technologies for the production of nitrogen-containing compounds from renewable feedstocks through the use of advanced engineering of microorganisms. (Prof. dr. Arnold Driessen, University of Groningen; Prof. dr. Isabel Arends, Delft University of Technology)
  3. Bioconstructions
    explores the use of biotechnology as an engineering tool to produce physical structures focused on civil and geo engineering. (Dr. Wouter van der Star, Deltares)
  4. Recycling of rare resources
    aims to improve the efficiency of resource recycling through microbial processes: ranging from improvements on commercial nutrient and metal recovery processes to optimization of bio-inorganic processes. (under development)
  5. Bioprocess Pilot Facility
    BE-Basic is working on the development and operation of a unique open innovation, multi purpose Bioprocess Pilot Facility (BPF). This facility will be available for development, testing, demonstration and training purposes, with a well trained crew and management, working at industry standards. The BPF offers room for pre-treatment and mid scale fermentation, large scale fermentation and downstream processing as well as future innovations in these areas.
  6. Synthetic Biology
    Develops tools and techniques for the improvement of micro-organisms. Design and optimization of novel pathways to desired products is complimented by unique cell membrane engineering aiming for efficient product export and improved robustness of the production organisms. develops tools and techniques for the improvement of micro-organisms. (Prof. dr. Bert Poolman, University of Groningen; Dr. Ton van Maris, Delft University of Technology)
  7. High-throughput experimentation and (meta)genomic mining
    aims to develop and apply high-throughput approaches and tools to explore and mine these untapped resources and to engineer and screen enzymes and other products for improved properties. (Prof. dr. Hans van Veen, NIOO-KNAW; Prof. dr. Dick Janssen, University of Groningen)
  8. Environmental impact of chemicals, bio-based molecules and processes
    develops novel and efficient methods for the evaluation and improvement of chemical safety in the bio-based economy. (Dr. Bart van der Burg, BioDetection Systems; Prof. dr. Hauke Smidt, Wageningen UR)
  9. Societal Embedding of a Biobased Economy
    This flagship aims to optimize the societal embedding of the products and processes developed by BE-Basic. This entails the identification of socio-economic aspects and sustainability issues, the development of adequate systems to monitor and model these and the development of effective and efficient education, communication and societal valorisation programmes. This work is carried out in an international setting which involves BE-Basic in several global initiatives, notably the Global Biorenewables Research Society, with partners such as the University of São Paulo (Brazil), Imperial Collge (UK) and the Energy Biosciences Institute (USA). (Prof. dr. Patricia Osseweijer, Delft University of Technology)

The department of toxicogenomics particiates in flagship 8 with the project Human HepG2 liver cell transcriptomics model

Project summary:

Testing for genotoxicity and carcinogenicity in vivo is done by repeated dose rodent assays which give high rates of false positive outcomes and costs many animal lives. In order to reduce consumer’s and patient’s health risks and environmental burden, development of innovative, better reliable, non-animal test methods for hazard and risk assessment of carcinogenic and genotoxic potency of chemical compounds is thus urgently needed. In this demonstration project we will generate a whole genome-transcriptomic response in HepG2 cells, ultimately focusing on the development of HepG2 reporter gene sets for carcinogenicity/genotoxicity prediction. In addition to our own transcriptomic analyses, we will position this project internationally, by setting up, collaboration with the US EPA’s ToxCast™ project, that will provide (sub)chronic animal exposure toxicity data and in vitro endpoints induced by genotoxic and nongenotoxic agents. By applying advanced integrative statistics, this unique approach will enable us to functionally anchor the obtained gene expression data for identification of the most relevant toxicological pathways. In collaboration with the VU and BDS comparison of our results with transcriptomics responses obtained in lower species will offer the opportunity to assess whether these genotoxic and carcinogenic pathways are evolutionary conserved which will demonstrate the biological plausibility of their relevance. These gene expression profiles can be used as a human liver-based predictive transcriptomic tool enabling safety evaluations of novel biobased industrial compounds to be developed within BE-BASIC. Together with BDS this gene set can then be patented, and further validated and developed into high throughput reporter gene assays for the detection of genotoxic and carcinogenic compounds which thereupon will be commercialized, for servicing safety assessment of pharmaceuticals, cosmetics, foods and industrial chemicals, as well as for monitoring waste streams, soils, surface and drinking water.

Associated Staff

Prof JCS Kleinjans PhD
Professor

Prof. Kleinjans studied biology at the Catholic University of Nijmegen and took a training in general biology and further trainings in physiological p more ...

DGJ Jennen PhD
Assistant Professor

Dr. Danyel Jennen is Assistant Professor in the field of toxicoinformatics at the UM Department of Toxicogenomics and he heads its core unit on toxico more ...

RAJ Schlooz BSc
Project Manager

Rob Schlooz graduated in Business Economics in 2001 at the Hogeschool Zuyd. He has worked for a year at the administrative department of a hotel in Ma more ...

MHM van Herwijnen BSc
Technician

Marcel van Herwijnen studied common-microbiology at the technical school in Eindhoven. This study consists off different aspects such as microbiology, more ...

R Cavill PhD
former staff

Since obtaining her PhD from the University of York in 2006, Rachel has worked as a bioinformatician, in Aberdeen, at Imperial College London and more more ...