PHD IN MICROBIOLOGY, MICROSCOPY AND BIOINFORMATICS (4 years, full-time)
Type of research Experimental/Bioinformatics (PhD)
Are you looking for a PhD position at the intersection between microbiology, fluorescence microscopy and bioinformatics? Do you enjoy developing new methods and performing microscopy, quantitative biology and modelling? Our group (A-Life & AIMMS, VU Amsterdam) in Amsterdam NL, is accepting applications for a 4 years fully-funded PhD position starting no later than February 1st 2023. Please apply at Vrije Universiteit Amsterdam (VU).
Candida albicans is an opportunistic fungal pathogen estimated to be present in 40-60% of healthy adults. However, in subjects with underlying disease, C. albicans increases its virulence, multiplies and causes deadly systemic infections. C. albicans virulence is linked to its ability to change morphology and to switch from a single cell yeast form to a filamentous pseudohyphal or hyphal form that can result in adhesive multicellular drug-resistant structures called biofilms. In C. albicans, the biofilm state is both sword and shield; it allows evasion of the immune system and invasion of host tissue and ultimately the bloodstream, leading to systemic infections with devastating consequences for the host. Its adaptability and versatility is what makes C. albicans such a successful pathogen and a challenge for drugs that often target only one of albicans’ morphological states, but not the community as a whole. At the basis of this limitation lies a lack of understanding of the underlying principles of C. albicans differentiation, which allows this fungus to tailor the heterogeneous composition of biofilms. Understanding the molecular mechanisms controlling the dynamic and reversible transitions between morphological states is therefore a challenge of the medical microbiology field, whose urgency is exacerbated by the appearance of novel drug-resistant Candida species.
The aim of this project is, therefore, to advance our understanding of C. albicans morphogenesis and biofilm development. Unlike previous studies, we use single cell technologies that allow us to characterize yeast, pseudohyphae and hyphae with high spatial and temporal resolution. To do so, we adapt the quantitative molecular imaging toolbox that we previously developed for the fungus S. cerevisiae and we develop single-cell approaches specific for C. albicans, to unravel the heterogeneity, organization and functioning of biofilms.
The long-term goal is to advance our understanding of fungal differentiation and set the basis for future studies investigating multispecies microbial biofilms and to overcome a fundamental challenge of infectious disease medicine: effective clearance of recalcitrant and biofilm-forming fungal infections.
you develop methods for multiplexed single molecule RNA FISH for C. albicans and study C. albicans differentiation
you develop fluorescence-based reporters to investigate cell signaling in single C. albicans cells
you develop imaging analysis and modelling approaches to study the spatial organization of gene expression in C. albicans yeast, pseudohyphae and hyphae
you communicate your research at local and international conferences
you are actively involved in both experimental and bioinformatic research
you publish your results in peer-reviewed journals and in a PhD dissertation
you have a MSc or equivalent degree in Molecular biology, Biophysics, Bioinformatics, Systems Biology, Microbiology or a related field, with a strong interest in microscopy and data analysis
you have experience with imaging analysis and programming software such as Python/R studio/MATLAB
you have excellent communication skills in both written and spoken English
Experience with Candida albicans is preferred, but any experience in microbiology and living systems is also appropriate. Prior experience with advanced microscopy techniques, including the use of fluorescence wide field and confocal microscopy is an advantage!
WHAT ARE WE OFFERING?
A challenging position in a socially involved organization. The salary will be in accordance with university regulations for academic personnel and amounts €2,541 (PhD) per month during the first year and increases to €3,247 (PhD) per month during the fourth year, based on a full-time employment. The job profile: is based on the university job ranking system and is vacant for at least 1 FTE.
The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 4 years. Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:
a maximum of 41 days of annual leave based on full-time employment
8% holiday allowance and 8.3% end-of-year bonus
solid pension scheme (ABP)
contribution to commuting expenses
discounts on collective insurances (healthcare- and car insurance);
Are you interested in this position?
Please apply via the application page and upload your curriculum vitae and cover letter until 31/08/2022 23:59.
Applications received by e-mail will not be processed.
If you have any questions regarding this vacancy, you may contact:
Name: Dr. E. Tutucci
Position: project manager
Duration of project
As soon as possible, but no later than February 1st 2023