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
Internship positions available in 2024
Filamentous Growth and Biofilm formation in S. cerevisiae and C. albicans resolved by single cell imaging
Experimental (Master)
Evelina Tutucci (evelina.tutucci@vu.nl)
Background
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
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: https://www.tutuccilab.com/research) 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.
Planned activities (and methods)
During this project, you will learn how to cultivate filamentous fungi, various molecular biology techniques as well as smFISH and cutting edge fluorescence microscopy approaches. You will also be trained in imaging analysis, which will be used to investigate gene expression (RNA spot counts) of cells in biofilm. 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 . You will participate and present in our Single-cell group meeting and Journal club.
Duration
6 Months
Starting date
From February/March 2024
Developing smRNA FISH for the identification of antibiotics-tolerant persister bacteria
Experimental (Master)
Evelina Tutucci (evelina.tutucci[at]vu.nl)
Wilber Bitter (w.bitter@vu.nl)
Frank Bruggeman (f.j.bruggeman@vu.nl)
Motivation
Multi-drug-resistant, pathogenic bacteria threaten human health. They have acquired DNA mutations that make them insensitive to antibiotics. Pathogenic bacteria are also successful in dealing with antibiotics, and the human immune system, because they often can switch to a non-growing, antibiotics-tolerance state, called the ‘persister’ state. Persister cells are formed from growing bacteria, can switch back to the growing state and coexist with growing cells in cell cultures. Since persister cells are not growing, they can withstand the effects of antibiotics that kill growing cells. It has been shown that growing cells can switch into persister cells, via so-called toxin-antitoxin systems. Such systems have been discovered in Escherichia coli and have since been found in many pathogenic bacteria, including Pseudomonas aerogenosa and Mycobacterium tuberculosis. Understanding how persister cells form is an important research topic.
Aim of this project
Since persister cells derive from growing cells and coexist with them in growing cell culture, we require single-cell methods to identify persister cells. One promising method is to determine the relative number of toxin and antitoxin transcripts in single cells, as it is believed that an excess of toxins over antitoxins turn growing cells into persister cells. The aim of this project is develop single-molecule RNA FISH, which allows for counting of the number of transcripts in single cells, for identification of persister cells. First in Escherichia coli and subsequently in Mycobacterium segmatus, a relative of M. tuberculosis.
Methods and techniques
fluorescence microscopy, molecular biology, bacterial cell cultivation, RNA methods, smRNA FISH.
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
1
Duration of project
6 months
Starting date
From July 2024