Open Positions

We are always welcoming enthusiastic and curious scientists!

Below, you can find the updated list of positions available in the group. If a PhD or Postdoc position is not advertised, but you are still interested in joining the team, please inquire about potential fellowship opportunities.

For more information, please contact Evelina Tutucci – evelina.tutucci@vu.nl

PhD position

Project title

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).

Project Description

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.

Your duties

  • 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


Requirements

  • 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);

Application

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.


https://workingat.vu.nl/ad/phd-in-fungal-biology-and-microscopy/l99bsb


Applications received by e-mail will not be processed.


Vacancy questions

If you have any questions regarding this vacancy, you may contact:


Name: Dr. E. Tutucci

Position: project manager

E-mail: evelina.tutucci@vu.nl


Duration of project

4 years

Starting date

As soon as possible, but no later than February 1st 2023

Master internship positions

Project title

Filamentous Growth and Biofilm formation in S. cerevisiae and C. albicans resolved by single cell imaging

Type of research Experimental (Master)

Supervisor(s)

Evelina Tutucci (evelina.tutucci[at]vu.nl)

Motivation

Many fungi such as Saccharomyces cerevisiae or Candida albicans are able to switch between a unicellular (yeast) form to a multicellular filamentous form in response to changes in the environment (e.g. nutrients availability, stress). This morphological transition allows fungi to adopt different survival strategies and in some instances become pathogenic. During filamentous growth cells acquire an elongated shape and unipolar budding pattern, allowing for greater exploration of the environment. A more advanced strategy is the formation of biofilms, multicellular structures that consist of different cell types (both yeast form and filamentous form) as well as an extracellular matrix, offering both increased structural integrity and resistance to antifungal drugs. While many of the genes required for this differentiation process have been identified through bulk analysis (e.g. RNA seq), their expression in single cells and during differentiation has remained largely unstudied.

Aim of this project

In this project, we investigate at the single cell level, the gene expression changes occurring during fungal differentiation. By using a fluorescence-based RNA imaging technique called smFISH (see pictures here) we visualize and quantify individual mRNA molecules in single cells to investigate the spatiotemporal control of gene expression during filamentation. Furthermore, we investigate how the spatial organization of cells in biofilms influences gene expression. We will measure cell-to-cell heterogeneity and couple it with spatial information, cell volume and cell length in filamentous cells. Since the microscopy data is very rich of information it will be possible to further expand the analysis, depending on your computational skills and your curiosity.

A prior familiarity with programming languages such as Python and R is a must.

Methods and techniques: fluorescence microscopy, molecular biology, fungal cells cultivation, RNA methods, smRNA FISH. You will participate and present in our Single-cell group meeting and Journal club.

Impact

During this project you become familiar with state-of-the-art methods of microbiology, molecular biology and fluorescence microscopy that are used throughout molecular biology labs in hospitals, academia and industry. Since smRNA FISH is not routinely used in such labs, the expertise which you acquire during this project will count on the job market, regardless whether this concerns a fundamental or applied job.

Number of positions available

2

Duration of project

6 months

Starting date

July 2022