Short Term Fellowships

High throughput screening toxicity in vitro methods for testing of selected chemicals and nano-particles in mixtures.

Research will assess applicability of experimental high throughput screening (HTS) methods for the assessment of toxicity of nano-particles and of a standard Water Framework Directive (WFD) list of compounds (both single and mixtures) using several protocols (Tetrahymena species, rat hepatoma cells (H4IIE), transfected yeasts cells (S. cerevisiae) with the human estrogen receptor (hER α)).

The results of the experiments with WFD-list compounds will be important to compare their toxic effects in the bulk state with those of nano-particles and to better understand their mode of action. This will allow better to understand which factors govern their behaviour and bioavailability as well as the toxicological effects of the chemicals and materials tested.

Successful candidates start at the next possible timepoint, but not later than September 2010.

Qualifications Your Qualifications:
- Master / diploma in chemistry, biology, biochemistry, geoecology
- Profound experience in cell culture work
- Some background in analytical chemistry involving ideally GC-MS and isotope dilution techniques
- Strong interest in molecular ecotoxicology, particularly also in in-silico screening techniques
- Interest to work in an interdisciplinary environment involving interactions between chemistry, biology, modelling, and health.
- Highly motivated for the project, like to work with others, integrate into a team

Formal applications should be exclusively send electronically and should include:
- Full CV and non German citizenship
- A statement of motivation (not more than one page)
- Copies of relevant exams, grades, master thesis work or publications
- Contact information of two reference persons
- Interest and willingness to stay in Turkey for at least 6 months for field work

For more details contact Prof. K.-W. Schramm

The ECO Evaluation of QSAR/QSPR modeling performance of some novel molecular descriptors.
12 months (3 positions of 4 months each)

Several new molecular descriptors have been defined in the last few years; however, their role in QSAR/QSPR modelling was not explored at all or was evaluated only by means of simple few benchmark datasets.
Therefore, some efforts need to be addressed to obtaining more knowledge about chemical information encoded by these molecular descriptors, their correlation with other well-known descriptors and their ability of predicting some properties of substances.
The molecular descriptors that are going to be considered in this study are:

1. Some topological indices calculated from generalized graph-theoretical matrices based on different weighting schemes of molecular graphs,
2. TDB descriptors, which are autocorrelations that also incorporate geometrical distances between atoms,
3. ETA descriptors, that encode electronic information,
4. surface and volume descriptors,
5. new substructure descriptors and fingerprints.

These molecular descriptors may hopefully improve models for prediction of environmental properties of interest. Therefore, experimental data will be collected from literature or existing open databases for different partition coefficients, vapor pressure, water solubility, bioconcentration factor, biodegradation, athmospheric oxidation, and so forth. Predictive models will be developed and compared with the models based on the EPA software (Episute).

For more details contact Prof. R. Todeschini

The ECO Methods for selection of structural features that influence substance toxicities.
10 months

Nowadays, substances can be computationally represented by several thousands of molecular descriptors which are numbers encoding structural features of them. Thanks to this huge amount of molecular descriptors, more chemical information is available to study substances from different points of view; however, when the aim is to generate robust predictive models for properties of substances, these are usually based on a few molecular descriptors and thus the problem here is how to select the most predictive ones. To this concern, it must be noted that the presence in a model of not relevant molecular descriptors doesn't play a neutral role, i.e. no influence in the model quality, but, on the contrary, it contributes to increase noise in the model and then to lower its predictive ability.
Two basic approaches are defined in literature: variable reduction and variable selection. The former is based on reduction techniques of descriptors without considering the response being modeled and are, basically, founded on the analysis of internal correlation among descriptors. In the latter approach, descriptors are selected considering the response being modeled. Genetic algorithms, in their different forms, step-wise procedures, descriptor annihilation in latent variable techniques are some of the algorithms used to select the most relevant descriptors in QSAR/QSPR modelling.
The main goal of this STF will be to study toxicological properties of substances by using both variable reduction and variable selection approaches. In particular, the study will focus on binary endpoints like active / no active and different techniques will be applied and compared, such as logistic regression, GA-KNN, substructural analysis, cluster significance analysis, together with the most common ones.
The choose of the environmental properties of interest will be performed considering the data produced from the other Partners of the ECO Project.

For more details contact Prof. R. Todeschini

Institute for Agricultural and Food Research and Technology, Madrid

INDUCTION OF OXIDATIVE STRESS IN MAMMALIAN AND FISH CELL LINES
The group of Endocrine Disruption and Toxicity of Contaminants wishes to appoint for 10 months a Short Term Researcher

The Spanish National Institute for Agricultural and Food Research and Technology (INIA) is an autonomous Public Research Organization (OPI) belonging to the Ministry of Science and Innovation (MICINN) in Spain. The INIA is responsible for the management and coordination of agrifood R&D programs at the national level, as well as of the execution of its own research programs, within the National R&D programs at the national R&D&i Plan or others. At the INIA, the activity of the Department of Environment focuses, among others areas, on Ecotoxicology and Environmental/Ecological Risk Assessment of potentially polluting activities. One important part of the work of the Department consists in the scientific support to the activities of different ministries (Ministry for Environmental and Marine and Rural Affairs). In the Department of Environment, the group EDTC (Endocrine Disruption and Toxicity of Contaminants) is interested in the particular mechanisms by which some toxics cause specific toxicity. The main tools used by the group are based on in vitro culture of some fish cells and cell lines. The knowledge obtained in the laboratory is applied to the detection of contaminants in the field and to the environmental risk assessment of chemicals.

Job description:

Oxidative stress generated in cells after exposure to a variety of toxicants is one of the major causes of toxicity. In this process, cells defend from the formation of reactive oxygen species (ROS) that could cause cell damage by means of different mechanisms involving glutathione and the induction of a variety of genes. Although these processes and the cross talk with cellular detoxification pathways are well characterized in mammals very few is known in fish. Currently, the research group offering this position is working on the induction of oxidative stress in fish cells and the relationship with other cellular detoxification pathways. The student will research on the induction of ROS after exposure to a selected group of contaminants in fish cell lines, and on the presence and the role played by detoxification pathways similar to those acting in mammals.
We are looking for a highly motivated candidate, with capabilities to work independently but in an interdisciplinary and international environment. Education in Biology, Biochemistry or related fields will be necessary and knowledge of Molecular Biology techniques desirable.

Job Requirements:

• Applicants are expected to have a university degree (MSc),
• Applicants must be in the first four years of their career in research,
• Applicants must be proficient in spoken and written English.

Conditions of Employment:
Employment conditions (salary, living expenses, travel expenses, etc.) are in accordance with the current Spanish regulation for public contracts and the requirement set forward by the Marie Curie programme. Duration of the contract: The successful applicant will be appointed for one year.
As this position is within a Marie Curie Initial Training Network, the following specific conditions with regard to the eligibility of candidates apply:
The researcher shall not be a national of a State in which the beneficiary's research team appointing him/her is located. In the case of a researcher holding more than one nationality, he/she will be able to be hosted by a beneficiary located in the country of his/her nationality in which (s)he has not resided during the previous 5 years.
At the time of appointment, the researcher may not have resided or carried out his/her main activity in Spain for more than 12 months in the 3 years immediately prior to his/her appointment. Short stays such as holidays are not taken into account.

For more details contact Dr. J.M. Navas

Investigation of the influence of chemical speciation on the accuracy of QSPR/QSAR models.

The biological activity and fate properties of chemicals can drastically change (in order of many orders of magnitude) depending on whether ionic or neutral forms of molecules are present in the environment. The difficulties with this task are frequently connected to low accuracy of existing methods to predict dissociation constants of molecules. The pKa model (which is under development within the GO-Bio grant) or otherwise calculated dissociation constants and/or experimental dissociation constants of molecules will be used to address this question and explore whether use of chemical speciation can increase accuracy of QSPR/QSAR models.

For these positions strong programming skills in Java or/and C++ are expected. The students should be able to implement & develop new chemoinformatics algorithms (calculation of descriptors, machine learning algorithms, etc.). Background in chemistry or bioinformatics, informatics, computer sciences is required.

For more details contact Dr. I.V. Tetko

In addition to clearly defined projects, there is the possibility of projects at free choice in each working group.
3 to 12 months

In this case you are asked to provide a short abstract about the topic of your PhD thesis and the sub-project you propose for ECO. Please, show the connection of the proposed project to the approaches and aims of REACH and its importance for future environment. Your motivation letter should also include the expected results, your expectations to the ECO training programme as well as your future career plans.

For more details contact
Dr. I.V. Tetko, Prof. K.-W. Schramm, Prof. W. Peijnenburg, Prof. T. Öberg, Dr. J.M. Navas, Prof. A.J. Hendriks, Prof. R. Todeschini or Prof. T. Knepper