September 18, 2024
PhD fellowship in Hologenomics at the Afekta Technologies Ltd, Kuopio, Finland
We are looking for a highly motivated and dynamic candidate to fill a 3-year fully funded PhD fellowship as part of the EU-funded, Marie Skłodowska-Curie Doctoral Network ‘HoloGen: Advancing the development and implementation of hologenomics in biological sciences’.
HoloGen is a MSCA Doctoral Network that will train the next generation of researchers in the emerging field of hologenomics. Microorganisms living in and on animal hosts impact nearly every biological process, and hologenomics aims to uncover how hosts and microbes interact. Understanding these interact will transform fields from basic biology to applied science in agrobiology, biomedicine, and more.
HoloGen brings together experts from 18 partners across Europe (universities, research institutes and industry), and will combine expertise in symbiosis biology, microbial ecology, computational biology, and more. The network will offer the successful candidates an unprecedented learning environment, including a common training program and research visits to both academic and industry partners.
For more information, see https://www.hologen-network.eu.
Project description
Adaptive processes to environmental changes are the central axis of evolution. Understanding how living organisms manage to adapt to environmental changes has become more relevant than ever, due to the intensity of the climate change we are experiencing. Various theories and experimental data suggest that vertebrates will be one of the taxa most affected by rapid climate change, due to their limited capacity to accumulate mutations that can be subject to natural selection. Therefore, most vertebrates depend on their phenotypic plasticity (through changes in behaviour and physiology) to adapt to new conditions. Although historically the origin of such plasticity has been attributed to genetic factors, recent studies have shown that the intestinal microbiota can grant extra plasticity under certain conditions. Therefore, the objective of the fellowship is to measure the degree of extra capacity that the microbiota confers to newts to adapt to different climatic conditions.
Animals and their gut microorganisms are known to interact continuously, yet how these interactions vary through time is still largely unknown. A powerful approach to address this is to jointly analyse the variation of genes, transcripts, proteins and metabolites produced by both animals and associated microorganisms across time. The doctoral candidate will study multi-omic dynamics based on data generated through shotgun sequencing and non-targeted metabolomics when subjecting laboratory outbreds to concatenated environmental variations (e.g. temperature, diet, energy intake, antibiotic treatment). Microbial metagenomic, metatranscriptomic, metaproteomic and metabolomic data will be generated from faecal samples, while host transcriptomic, proteomic and metabolomic data will be generated from blood.
Our group and research
We offer an exciting position and a chance to do research at the intersection between industry and academia. Afekta Technologies Ltd. is a science-driven company established in 2017. Afekta offers metabolomics analysis services for various research purposes across life sciences. We have specialized in metabolomics analyses related to food, nutrition, and gut microbiota. Afekta has experience in being a beneficiary in several Horizon 2020 projects including previous Marie-Sklodowska-Curie Doctoral Network actions. To learn more about Afekta please visit www.afekta.com.
Academic studies related to the position will be done at the University of Eastern Finland (UEF), which will also award the PhD. UEF is a multidisciplinary university with a strong focus on life sciences. UEF has around 16,000 students and 3,000 staff members. The doctoral student will be enrolled to the graduate school at the Faculty of Health Sciences. General information about PhD studies at the Faculty can be found at https://www.uef.fi/en/faculty-of-health-sciences. Office and laboratory spaces of Afekta Technologies are right next to the UEF campus in Kuopio. Finland. Kuopio in particular, is a safe, clean and technology-driven place known for its superb education and welfare know-how. To learn more about UEF and life in Finland visit https://www.uef.fi/en/life-in-finland.
Principal supervisors
Prof. Kati Hanhineva is research director and group leader of the Food and Nutritional metabolomics research group (hanhinevalab.com). The group has long-term expertise in developing LC-MS based metabolomics analytical and data-analytical methods, as well as applying them on various research questions typically revolving around the topics related to food, nutrition, health effect and gut microbiota. Dr Olli Kärkkäinen, CEO at Afekta Technologies and senior researcher in drug toxicology (School of Pharmacy, University of Eastern Finland) has a title of docent in pharmacology and toxicology and is expert in the study of effects of external exposures, like drugs, toxins and nutrition, to the metabolic processes in the body using data from in vitro, in vivo, clinical trials and epidemiological cohorts.
For further information on the position, please contact Prof. Kati Hanhineva (kati@afekta.com) or Dr Olli Kärkkäinen (olli@afekta.com).
Start: 01/01/2025 or as soon as possible
Duration: 3 years as a PhD fellow
Mobility rule: According to the MSCA mobility rule, the applicants must not have resided or carried out their main activity (e.g., studies, work, research) in Finland for more than 12 months in the 3 years immediately prior to the call deadline.
Job description
Your key tasks as a PhD fellow at Afekta are:
- Carrying through an independent research project under supervision.
- Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
- Participating in all training activities organised within the DN HoloGen.
- Participating in active research environments including a stay at another research team.
- Obtaining experience with teaching or other types of dissemination related to your PhD project.
- Teaching and disseminating your knowledge.
- Writing a PhD thesis on the grounds of your project.
Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a Master’s degree related to the subject area of the project, e.g. biomedicine, pharmacy, toxicology, analytical chemistry, microbiology, data science, bioinformatics or similar. Please note that your Master’s degree must be equivalent to a Finnish Master’s degree.
Other important criteria are:
- You have documented experience in analysing mass spectrometry and/or omics data.
- You have experience using R.
- You have experience in writing research articles and giving scientific presentations.
- You have proficient communication skills and ability to work in teams.
- You have excellent English skills written and spoken.
Application procedure
Your application must be submitted at the latest 30th October via e-mail to kati@afekta.com including the following documents in PDF format:
1. Motivation letter (max. one page)
2. CV incl. education, experience, language skills, publications and other relevant information for the position
3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Finnish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your Master’s degree must be equivalent to a Finnish Master’s degree.
The application deadline is October 30, 2024.