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Early Stage Researchers 

11 Early Stage Researchers (ESR) will be employed in MICROMETABOLITE ITN Project.

Each ESR will receive comprehensive and multi-faceted training in general and transferable skills, scientific know-how and technical skills by :

  • local training at the host institution benefiting from direct supervision and doctoral schools
  • secondments of 9 months in 4 to 5 institutions
  • participation in up to 9 network-wide trainings and 3 summer schools
  • attendance of at least 2 international conferences with presentations (talks or posters)

Each ESR will be exposed to academic and non-academic environments. ESRs hosted by academic beneficiaries will be seconded to industry partners for at least 4 months. ESRs hosted by non-academic beneficiaries will be seconded to another industry partner for 3 months with most of the secondments being spent in academia. Thus, ESRs will be made familiar with different academic and industry settings across Europe in a well-balanced manner.  


ESR1: Cintia Csorba

Host institution: Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources

Supervisor: Dr. Angela Sessitsch, Dr. Günter Brader

Cintia studied Cell biology and Molecular biology at the University of Szeged, Hungary. After her graduation in 2015, she obtained a master’s degree in Molecular biology and Microbiology also in Hungary, at the University of Szeged. Her work during the master's thesis project, at the Bay Zoltán Foundation for Applied Research, was mainly focused on bioremediation of fuel-additives with ether-degrading microorganisms in contaminated soil and groundwater.

Project title: Interaction between microbes and secondary metabolite production of medicinal plants.

Objectives: (1) To study the succession of root-associated microbial communities of Boraginaceae plant species during plant development and to identify taxa that correlate with high secondary metabolite production (2) To study root-associated microbiomes associated with Boraginaceae plant species and to correlate microbial community structures and plant genotype with metabolome characteristics (3) To screen microbial endophytes for increasing metabolite production and plant growth.

Starting date: 02/10/2017


ESR2: Muhammad Ahmad

ESR2

Host institution: Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources

Supervisor: Dr. Eva Maria Sehr

Ahmad studied Agriculture with specialization in Plant Pathology at the University of Agriculture Faisalabad, Pakistan. After his graduation, he pursued two master’s degrees: i) Tropical Forestry (Technical University Dresden, Germany) and ii) Crop Protection (University of Gottingen, Germany). In his master's thesis project, he investigated the biosynthesis and defensive role of plant secondary metabolites (Flavan-3-ols and Proanthocyanidins)

Project title: Transcriptomics of interactions between Boraginaceae and microorganisms

Objectives: (1) To genotype sampled plants by SSR analytics. (2) To extract high quality total RNA of Boraginaceous root tissue and microorganisms. (3) To apply RNA-Seq for studying effects of selected microorganisms on transcriptome profiles of treated versus untreated plants. (4) To reveal differentially expressed genes possibly involved in pathways leading to enhanced production of A/S via RNA sequencing and diverse well-established bioinformatics tools.

Starting date: 03/04/2018


ESR3: Yanyan Zhao

ESR3

Host institution: Université catholique de Louvain, Earth and Life Institute, Laboratory of mycology (ELIM)

 Supervisor: Prof. Stephan Declerck and Dr. Ismahen Lalaymia

Yanyan studied Horticulture Science at the Agriculture University of Hebei, China. After her graduation in 2014, she obtained a joint master’s degree in International Horticulture Science at the University of Bologna (Italy), Technical University of Munich (Germany) and Free University of Bolzano (Italy). Her work during the master's thesis project, at the Phytobacteriology lab in University of Bologna, was mainly focused on molecular detection and characterization of phytoplasmas infecting paulownia and jujube in China.

Project title: Fungal diversity assessment and impact on plant growth and metabolites production

Objectives: (1) To isolate and identify arbuscular mycorrhizal fungi (AMF) and fungal endophytes associated with Alkanna tinctoria and Lithospermum erythrorhizon from the wild and in the field. (2) To assess the fungal community composition in A. tinctoria and/or L. erythrorhizon from the wild. (3) To preserve AMF and fungal endophytes from A. tinctoria and L. erythrorhizon and related plants under the more adequate conditions. (4) To test and evaluate the role of AMF and fungal endophytes on plant growth promotion and root colonization. (5) To evaluate the role of AMF and fungal endophytes on plant metabolites production.

Starting date: 02/10/2017


  ESR4: Annalisa Cartabia

Host institution: Université catholique de Louvain, Earth and Life Institute, Laboratory of mycology (ELIM)

Supervisor: Prof. Stephan Declerck and Dr. Ismahen Lalaymia

Annalisa studied Agricultural Science and Technology at the University of Milano (Italy). After her graduation, she pursued a master’s degree in Crop Science at the same University, during which she spent one semester as an Erasmus student at the Technische Universitӓt of München (Germany). Her work during the master’s thesis project was focused on the influence of light quality on flavonoid biosynthesis in in vitro apple plants.

Project title: A semi-hydroponic system associating plants and microbes for optimal secondary metabolites production

Objectives: (1) Select model organisms from the collections with known impact on secondary metabolites (SM) production and/or plant growth promotion. (2) Develop a semi-hydroponic system associating the above-mentioned microorganisms with Alkanna tinctoria and Lithospermum erythrorhizon. (3) Extend the system to microorganisms showing plant growth promotion and/or increasing SM production. (4) Evaluate microbial combinations on SM production in semi-hydroponics systems and to optimize SM production.

Starting date: 02/10/2017


ESR5: Evangelia Tsiokanou

ESR5

Host institution: National and Kapodistrian University of Athens, School of Pharmacy, Pharmacognosy and Chemistry of Natural Products (NKUA).

Supervisor: Nikolas Fokialakis, Assistant Professor

Evangelia studied Pharmaceutical Sciences at the Free University of Brussels (ULB), Belgium. After her graduation, she pursued her master’s degree in the NKUA (Greece), in the isolation, development, production and control of bioactive natural products. Her work during the undergraduate and postgraduate thesis projects was mainly focused on the phytochemical investigation of Citrus bergamia.

Project title: Investigation of bioactive secondary metabolites of Boraginaceae species.

Objectives: (1) To investigate the collected wild plants of A. tinctoria and related species from different locations in Greece and to isolate Alkannin and Shikonin. (2) To develop analytical methods based on high performance thin layer chromatography (HPTLC) (or Supercritical Fluid Chromatography - SFC) for the quantification of A/S contents. (3) To perform MS-based metabolic profiling of Boraginaceous plants collected from the wild, cultivated in vitro, by semi-hydroponics or field cultivation, to determine variation in metabolite production and identify known metabolites. (4) To de-replicate secondary metabolites and perform targeted isolation and identification of compounds induced by selected microorganisms.

Starting date: 04/12/2017


 ESR7: Alicia Varela Alonso

 ESR7

Host institution: Institut für Pflanzenkultur e.K.

Local Supervisor: Carolin Schneider and Philipp Rödel

Academic Supervisor: Stéphane Declerck, Full Professor Université catholique de Louvain.

Alicia studied Agricultural Engineering at the Polytechnic University of Madrid, Spain. After her graduation, she pursued a master’s degree in Agroforestry Biotechnology (Polytechnic University of Madrid). Her work during the master’s thesis project was focused on Isolation of allergens by chromatographic techniques and immunodetection (ELISAs and microarrays of several purified proteins).

Project title: Design of plant production systems for Alkanna tinctoria and Lithospermum erythrorhizon integrating microorganisms.

Objectives: (1) To establish in vitro propagation via shoot organ cultures of Boraginaceae collection. (2) To inoculate elite plant clones across the following scales: in vitro, acclimatization in greenhouse and field with a set of promising microbial strains. (3) To test in vitro induction of A/S in root and/or shoot organ cultures with e.g. copper sulfate and fungal elicitors. (4) To determine total A/S contents and their enantiomeric ratio under several cultivation and conditions and to optimize those.

Starting date: 1/10/2017


ESR8: Nebojša M. Rodić

Host institution: Aristotle University of Thessaloniki, School of Chemical Engineering, Organic Chemistry Laboratory

Supervisor: Andreana N. Assimopoulou, Associate Professor

Nebojša studied General Chemistry at the University of Novi Sad, Serbia. After his graduation, he pursued a master’s degree in Advanced Spectroscopy in Chemistry, in Germany and Finland, at Universität Leipzig and University of Helsinki. His work during the master’s thesis project was focused on multi-dimensional nuclear magnetic resonance techniques for probing protein-protein interactions.

Project title: Metabolomics analysis and determination of bioactive Alkannins/Shikonins in Boraginaceae species

Objectives: (1) To determine A/S contents in A. tinctoria / L. erythrorhizon throughout plant development and in microbe-associated plants. (2) To collect wild plants of A. tinctoria and related species from 15 locations in Greece (in collaboration with the University of Athens). (3) To perform DNA barcoding and to assess A/S contents, enantiomeric A/S ratio and metabolome characteristics. (4) To determine A/S contents in plants subjected to transcriptome analysis. (5) To determine A/S contents and enantiomeric ratios (and perform LC/MS and/or NMR based metabolic profiling) under several production conditions.

Starting date: 20/10/2017


ESR9: Athanasios S. Arampatzis

Host institution: Aristotle University of Thessaloniki, School of Chemical Engineering, Organic Chemistry Laboratory

Supervisor: Andreana N. Assimopoulou, Associate Professor

Athanasios studied Chemical Engineering at the Aristotle University of Thessaloniki, Greece. After his graduation, he pursued a master’s degree in Pharmaceutical Design and Engineering in Denmark, at the Technical University of Denmark (DTU). His work during the undergraduate and postgraduate thesis projects was mainly focused on liposomes as systems for delivery of bioactive molecules.

Project title: Biological activities & technological exploitation of Alkannin/Shikonin derivatives and Boraginaceae species.

Objectives: (1)To examine by MS-imaging the type of metabolites on infected or wounded sites with and without the application of A/S. (2) To perform metabolomics driven analysis for the determination of the effect of A/S derivatives on several pathologies (such as cancer) in vitro and/or in vivo. (3) To further technologically exploit A/S applications by developing and characterizing tissue engineering scaffolds as wound dressings infused with these bioactive molecules with several biomaterials. (4) To optimize and scale-up A/S derivatives by extraction and isolation.

Starting date: 18/10/2017


ESR10: Angélique Rat

Host institution: Ghent University, Faculty of Sciences, Dept. Biochemistry and Microbiology, Lab. of Microbiology

Supervisor: Anne Willems, Professor and Aurélien Carlier, Assistant Professor

Angélique studied the Classes Préparatoires BCPST (Biology

Chemistry Physics Science of the Earth) at Tours, France. She then pursued a degree in Engineering, specializing in Agronomy at the Institut National Supérieur des Sciences Agronomique, de l'Alimentation  et de l'Environement (Dijon, France) during which she spent one semester as an Erasmus student at the University of Natural Resources and Life Sciences, Vienna. Her work during her thesis project was focused search for biostimulants that improve the bioavailability of phosphorus to plants.

Project title: Isolation and functional characterization of root endophytic bacteria from Boraginaceae that promote growth and affect plant secondary metabolism.

Objectives: (1) To isolate and characterize endophyte and rhizosphere bacteria associated with Boraginaceae plants with high A/S production. (2) To characterize selected strains from  plants with high A/S content for plant growth promotion & colonization. (3) To evaluate the effect of bacterial strains on plant secondary metabolite production.

Starting date: 16/10/2017


ESR11: Henry Naranjo

ESR11

Host institution: Ghent University, Faculty of Sciences, Department of Biochemistry and Microbiology, Laboratory of Microbiology

Supervisor: Anne Willems, Professor and Aurélien Carlier, Assistant Professor

Henry got a BSc. in Biotechnology (ESPE, Ecuador) and in 2016 he obtained a MSc. in Cellular and Molecular Biotechnology (Wageningen UR, The Netherlands). His work during undergraduate and postgraduate studies was mainly focused on the field of microbiology, with physiology, ecology and genomics of bacteria being his main research interest.

Project title: Genomic and functional molecular characterization of root endophytic bacteria from Boraginaceae that promote growth and affect plant secondary metabolism

Objectives: (1) To characterize bacterial endophytes and rhizosphere bacteria associated with Boraginaceae plants with high A/S production. (2) To explore plant-microbe interaction pathways in selected representative strains via comparative genome analysis. (3) To identify and explore the diversity of selected significant pathways of plant-microbe interaction related to increased A/S production and plant growth.

Starting date: 15/03/2018