The Masterclass for MSCA Postdoctoral Fellow 2024 at the National Institute of Biology (NIB), Slovenia

Available project

Description of field and supervisors

MSCA Fellow in the field of nucleic acid analysis to advance measurements in microbiology for One Health initiative

Join our dynamic research team dedicated to advancing knowledge in bacteriology and metrology within the field of biology through the prestigious MSCA postdoctoral fellowship. As part of the Department of Biotechnology and Systems Biology, our research group, Bacteriology & Metrology, focuses on a wide range of topics related to the biology, diversity, and detection of pathogens. As a MSCA postdoc fellow in our research group, you will have the opportunity to contribute to cutting-edge research projects aimed at developing innovative approaches for the direct and indirect identification and quantification of microorganisms (EMPIR AntiMicroResist and SEPTIMET projects, Horizon project BeXyl, national projects BACTOMET, FungiMEt, Met4Lab, ProRef). These past and ongoing projects are crucial for advancing the standardization and harmonization of molecular diagnostics within the "One Health" concept, where human, animal, and environmental health are interconnected.

Led by renowned experts, we are an interdisciplinary team comprising biologists, microbiologists, biochemists, and biotechnologists. We specialize in developing molecular methods and are recognized as one of the leading European metrology laboratories in measuring nucleic acids. Our research utilizes state-of-the-art methods and technologies, including microscopy (fluorescent, electron), cell counting, flow cytometry, quantitative and digital PCR, high-throughput sequencing, and bioinformatics. These techniques are applied across various aspects of bacteriology and metrology, enabling us to address current challenges and develop new metrological approaches to tackle emerging issues in the field. In addition to our research, we actively participate in various European projects and networks, fostering collaboration and data exchange with other leading laboratories across Europe. This collaborative approach allows us to stay at the forefront of research and make significant contributions to the advancement of our research fields.

Location: Ljubljana

Supervisor: Alexandra Bogožalec Košir, Research Gate: https://www.researchgate.net/profile/Alexandra-Bogozalec-Kosir

MSCA Fellow in the field of virology

We are searching for a researcher who will work in a dynamic and internationally active research group using state-of-the-art molecular biology techniques for detection, surveillance and/or studies of biology, diversity, and evolution of viruses.

The researcher will work at the Microbiology unit of the Department of Biotechnology and Systems Biology (FITO). The department is committed to generate highest quality scientific knowledge about complex biological processes with an emphasis on interactions between pathogens and their hosts. This is achieved using state-of-the-art equipment, inclusion in European infrastructural centers, an established quality control system, and involvement in many European and other international projects. At Microbiology unit, we perform research spanning from biology, biodiversity, evolution, epidemiology, and diagnostics of microbes to development and validation of tools for their detection. We use state-of-the art techniques to address different research questions. Our research is focused on plant pathogens, but also other organisms pathogenic to human and animals, environmental virology, water-based epidemiology, and viral ecology (studies of viromes of organisms and environmental samples in an ecosystemic context). We are part of European reference laboratory for pests on plants (for viruses and phytoplasmas).

We seek for a candidate with PhD in biology / biotechnology / microbiology / bioinformatics / biostatistics / biochemistry or any other similar fields. Experiences in big data analysis, statistics, data visualization, bioinformatics and/or virology are beneficial. The candidate will work in a collaborative team (currently 15 people) environment comprised of senior researchers, laboratory associates, postdocs, PhD students and others. The exact topic and plan of the research work will be determined together with the candidate according to his skills, ideas, and ambitions within the ongoing research directions of the group. It will likely connect knowledge from different scientific fields, especially virology, biotechnology, and bioinformatics. Research will be aimed at understanding the diversity, survival, evolution, and role of viruses in ecosystems. In this, the researcher will use a range of classical and modern virology and molecular biology approaches, such as high-throughput sequencing (e.g., Illumina, Oxford Nanopore Technologies) with subsequent bioinformatic analysis of data, quantitative and digital PCR, electron microscopy, and biological infectivity tests.

Location: Ljubljana

Supervisor: Denis Kutnjak, Google Scholar: https://scholar.google.com/citations?hl=en&user=hS3qh8AAAAAJ&view_op=list_works&sortby=pubdate  

MSCA Fellow in Advancing Nucleic Acid Analysis Techniques for Life Sciences Applications

The Bacteriology & Metrology research group at the Department of Biotechnology and Systems Biology focuses on nucleic acid analysis, which is fundamental to many areas of the life sciences such as biotechnology, cell biology, genetics, microbiology and molecular biology. Nucleic acid analysis involves the detection, identification and quantification of nucleic acids from different organisms, often from different matrices. Our group uses nucleic acid analysis in research of biology and diversity of microorganisms and in applications such as diagnostics or the development of reference measurement methods. An important part of our expertise is metrology, where we develop the cutting-edge ability to support the reliability, comparability, and traceability of nucleic acid measurement results in microbiology and other sectors. Our research utilizes state-of-the-art methods and technologies for nucleic acid analysis, including various platforms for quantitative and digital PCR, high-throughput sequencing and bioinformatics, as well as complementary methods and technologies such as microscopy (fluorescence, electron), cell counting, flow cytometry and MALDI-TOF.

As an MSCA Postdoctoral Fellow you will work on a research project of your own design, in dynamic and interdisciplinary team of biologists, microbiologists, biochemists and biotechnologists involved in several national and international projects. We are recognized as one of the leading European metrology laboratories for the measurement of nucleic acids and have been partners in the European projects AntiMicroResist and SEPTIMET dealing with human microorganisms, while at national level we coordinated the ProRef project in support of plant health. We are currently coordinating the FungiMET project to identify biofilms in extreme environments. We actively participate in various networks (TraceLabMed, SSF, POLMO) and associations (EPPO, NAWG) fostering collaboration and data exchange with other leading laboratories in Europe and beyond.

Location: Ljubljana

Supervisor: Mojca Milavec, ORCID: https://orcid.org/0000-0002-5794-2109

MSCA Fellow in the field of Groundwater Ecology and Evolution

We are searching for a perspective postdoctoral candidate with a background in groundwater ecology, biodiversity or evolution.

Slovenia is one of the global hot spots of groundwater biodiversity with well investigated karstic groundwaters in Dinaric Region, while much less is known about porous aquifers extending in other parts of Slovenia. It is well known that hydrogeomorphology strongly underlines the groundwater biodiversity patterns in alluvial aquifers, less is known about coupling eco-evolutionary drivers of interstitial biodiversity patterns. The Sava River catchment is the largest catchment in Slovenia representing the longest “interstitial highway” and encompassing all three major aquifer types (i.e., karstic, fissured, alluvial). Hence, it represents a good model to investigate eco-evolutionary drivers of groundwater biodiversity patterns at regional scale. The detailed postdoctoral research program will be developed in collaboration with the chosen candidate and will offer the opportunity to the candidate to closely collaborate with international research teams through ongoing research project, DarCo - The vertical dimension of conservation: A cost-effective plan to incorporate subterranean ecosystems in post-2020 biodiversity and climate change agendas.

We are looking for a candidate with a passion for research, creativity, initiative, and the ability to work in an international team. Essential attributes include proficiency in English, ability to work in R and GIS environments, sound critical thinking, reliability, and a positive outlook.

Location: Ljubljana

Supervisor: Nataša Mori, ORCID: https://orcid.org/0000-0002-1168-305X

Co-supervisor: Cene Fišer (University of Ljubljana), ORCID: https://orcid.org/0000-0003-1982-8724

MSCA Fellow in the field of Cancer research and understanding aggressive primary tumors

Research focus of MSCA candidate will be assessment of the tumor microenvironment of aggressive primary tumors, such as brain and lung, using spatial biology techniques, in order to understand immunobiology and select potential biomarkers for more efficient treatment of cancer. Research will be related to the work and international involvement of Cancer Biology group.

Cancer Biology group has an excellent scientific output in the last decades, in particular in the field of understanding human brain tumors and its microenvironment, including the role of cancer stem cells and supportive microenvironment in the therapy resistance, and the development of novel therapeutic approaches against cancer. The group aims to understand aggressive primary tumors using state state-of-the-art approaches and methodologies in molecular and cell biology, including patient-derived 3D cellular models, confocal/light-sheet microscopy, and spatial biology approaches.

Current EU projects and associations: CutCancer (https://www.cutcancer.si/ ), GenomeMET (https://www.genomemet.org/), COST IMMUNO-model (https://www.immuno-model.eu/) and Net4Brain (https://net4brain-cost.eu/), EORTC (https://www.eortc.org/)

Location: Ljubljana

Supervisor: Metka Novak, ORCID: https://orcid.org/0000-0002-3041-1156

MSCA Fellow in the field of Immunology and cellular immunotherapy

Autoimmune diseases affect approximately 7.6-9.4 % of the world's adult population, with young and middle-aged women being affected more frequently than men. Standard first-line therapies include general immunosuppressants, which are often associated with adverse side effects and incomplete efficacy. Even with treatment, most autoimmune diseases gradually deteriorate patients' health, resulting in a reduced quality of life and a significant burden on the public health system.

Patients therefore need targeted, safe and effective therapies that eliminate or reduce dependence on immunosuppressive drugs, restore the immune response and possibly stimulate tissue repair. Modulation of the immune system through immunotherapies with autologous, genetically engineered immune cells is at the forefront of several paradigm-changing therapeutic approaches for the treatment of severe diseases for which there are limited or no therapeutic options.

In the context of adoptive cell therapies for autoimmune diseases, one of the promising approaches is the utilisation of regulatory T cells (Treg), which are one of the most important immune cells responsible for homeostasis and peripheral tolerance. Therefore, our and other efforts aim to manipulate Treg cells with transgenic T cell receptors (TCR) or CAR to make them specific for target antigens and tissues, thus increasing efficacy and persistence in target tissues while limiting off-target effects.

The candidate will be able to study Treg cell biology and establish a platform for genetic manipulation and assessment of cellular products and their complexity using multicolour spectral flow cytometry as well as state-of-the-art single-cell next-generation RNA sequencing methods that enable in-depth analysis of the transcriptome. We aim to introduce these techniques into the cellular product assessment platform and discover new elements that contribute to the suppressive function of Treg cells. We are interested in expanding our group with a postdoctoral researcher with an interest in immunology and experience in bioinformatics, ideally with RNA sequencing.

Location: Ljubljana

Supervisor: Jelka Pohar, ORCID: https://orcid.org/0000-0002-7616-164X

MSCA Fellow in the field of plant - environment interactions

The topic of the research work of the Postdoctoral Fellow will be on plant – environment interactions, as the Postdoctoral Fellow will join to a team of scientists with a long term research goal to answer the question which genes, proteins and signal molecules are of key importance for the resistance of agronomically important plants to the infection with pathogen microorganisms such as viruses and phytoplasmas, and to abiotic stresses such as drought and salinity with the analysis of sensitive and resistant varieties and of genetically modified plants. This topic is of high importance, especially as climate change is threatening the sustainability of agriculture, due to the recurrent drought events during the summer. Moreover, climate change is also influencing the availability of water resources, therefore the need for irrigation is increasing. Consequently, drought and salinity stress are becoming very important issues, as irrigation water may contain elevated salt concentrations. Moreover, climate change is also affecting plant - pathogen interactions as the outcome of the interaction depends on genotypes of both, host plant and pathogen and can vary with various environmental conditions and various developmental and physiological growth stages of a plant.

The research topic will be addressed using up-to-date cutting-edge methods and research equipment for bioimaging techniques (e.g. plant phenotyping, light, confocal and electron microscopy…), molecular biology (e.g. NGS, qPCR, ddPCR, CrisprCas…) and bioinformatics (including several licences and pipelines). The research work will be performed in completely new fully equipped labs, including plant growing facilities (e.g. research quarantine greenhouse and growth chambers for plants in soil and in tissue cultures).

Location: Ljubljana

Supervisor: Maruša Pompe Novak, NIB: https://www.nib.si/eng/index.php/component/directory/?view=details&id=104&Itemid=12

MSCA Fellow in the field of jellyfish-microbes interactions

Blooms of gelatinous zooplankton can represent a significant, but largely overlooked, source of organic matter (OM) in the ocean. In this context, jellyfish were recently recognized as important agents of carbon export to the ocean’s interior, highlighting the necessity of including jellyfish into ocean biogeochemical models. In particularly, since jellyfish will likely thrive under projected changes of oceanic habitats. The interactions between microbes, jellyfish and jellyfish-derived OM represent a knowledge gap that needs to be addressed to accurately incorporate jellyfish in ocean carbon budgets.

In this context we propose projects topics related (but not limited) to:

• 1) disentangling the biochemical complexity of the OM encapsulates and released by vast diversity of different jellyfish species at molecular level;
• 2) elucidating the fate of jellyfish detritus in the ocean to improve the flux estimates of jellyfish carbon and nitrogen to different depth layers of the oceanic water column and allow us to better constrain the amount of jellyfish biomass deposited at the seafloor and hence determine its impact on benthos;
• 3) link between microbes, jellyfish and jellyfish-derived OM using state-of-the-art approaches in marine microbial ecology, coupling -omics with the characterization of the OM pool at the individual compound level.

Location: Piran

Supervisor: Tinkara Tinta, ORCID: https://orcid.org/0000-0001-6740-8973

MSCA Fellow in the field of Ocean Modelling[TP1] 

“Computer simulations are our only way to experiment with the planet” (Cushman-Roisin and Beckers, 2011). Ocean circulation models are an extremely useful tool to study ocean dynamics, ranging from circulation processes, effects of climate change, extreme events, dense water formation, storm surges to tsunamis etc. They are an indispensable part of the Earth System models and therefore one of the key components in climate simulations. They can be used to provide short-term and long-term forecasts of the ocean state or, in combination with Lagrangian particle tracking, spreading of pollutants or provide support in search and rescue operations. Combining the Lagrangian approach with Individual Based Models opens an incredible array of possibilities to study the population dynamics of marine species. Such models are used to simulate the dispersal of larvae, animal migrations and connectivity between populations or e.g. marine protected areas. When coupled with biogeochemical models, the ocean circulation models provide a holistic overview, continuous in space and time, of the functioning of the marine ecosystem - from most basic principles to the lower trophic levels. Something none of the observational approaches are capable of.

Our main tools are CROCO (formerly ROMS_AGRIF) circulation model, OpenDrift software package for Lagrangian applications and we have coupled CROCO with BFM biogeochemical model in cooperation with the Jožef Stefan Institute. We have used our array of models to study the surface currents, dense water formation, spreading of pollutants, impact of offshore gas platforms on the jellyfish population dynamics, the dynamics of Pelagia noctiluca in the Mediterranean Sea, the impact of jellyfish bloom decay on the marine ecosystem etc. We were also involved in the development of the operational ocean modelling chain used in forecasts provided by the Slovenian Environment Agency.

Location: Piran

Supervisor: Martin Vodopivec, ORCID: https://orcid.org/0000-0002-0163-1264

MSCA Fellow in the field of Long-term data on the ecosystem dynamics and interspecific interactions

We are searching for postdoctoral candidate interested and skilled in the field of analysis of long-term population data and ecological modelling. We are conducting long-term studies especially in forest ecosystems stratified over the altitudinal gradient taking into account apex predators (owls), higher trophic level consumers (small mammals, birds) and lower trophic level consumers (beetles). We are seeking analytical support in assessment of these data for identifying interaction patterns within and between different trophic levels and guilds and changes in ecosystem functions under climatic influences. During our 20-year study of forest stands with apex predators, namely sympatric forest owls of the genus Strix, we have found previously unknown effects of the coexistence of raptors, apparently due to intense competition between them. The Tawny Owl (Strix aluco) and the Ural Owl (Strix uralensis) are closely related and despite the moderate difference in size they appear to be very similar in many aspects of their ecological niche and consequently strong competitive interactions between them have been observed, leading to nest displacement, competitive exclusion and pronounced spatial segregation. Their diet consists mainly of mice and voles, which determine their population fluctuations and reproduction, but in different way. The simultaneous population increase of both species is still not fully understood, and especially not in a way if such increase reflects in ecosystem changes most probably driven by altered small mammal population dynamics. Therefore the role of small mammals, namely mice, voles and dormice, is aimed to be explored in terms of effects on higher (owls) and especially on lower trophic levels (insects).

We are searching for postdoctoral candidate interested and skilled in the field of analysis of long-term population data and ecological modelling. We are conducting long-term studies especially in forest ecosystems stratified over the altitudinal gradient taking into account apex predators (owls), higher trophic level consumers (small mammals, birds) and lower trophic level consumers (beetles). We are seeking analytical support in assessment of these data for identifying interaction patterns within and between different trophic levels and guilds and changes in ecosystem functions under climatic influences. The candidate will join increasing research team at National Institute of Biology in Ljubljana with fieldwork options in pristine montane Beech forests characteristics for southern mountains in the Balkan Peninsula. The research team is referenced to the apex predator (owls) and insect ecology.

Location: Ljubljana

Supervisor: Al Vrezec, Google Scholar: https://scholar.google.si/citations?hl=sl&user=8eJUMegAAAAJ