PhD in Fungal Pathogens Biology, Microscopy and Bioinformatics

PhD position at the intersection between medical microbiology, fluorescence microscopy and technology development.

Your function

Are you looking for a PhD position at the intersection between medical microbiology, fluorescence microscopy and technology development? Do you enjoy developing new methods and performing microscopy, quantitative biology and bioinformatics? The Tutucci group (A-Life & AIMMS, Vrije Universiteit Amsterdam) in Amsterdam, NL is accepting applications for a 4 years fully-funded PhD position starting at the latest on November 1st 2024. Please apply at Vrije Universiteit Amsterdam (VU).

Your duties

  • you develop and perform RNA sequencing on C. albicans and A. fumigatus to identify tip-localized mRNAs
  • you develop and perform single molecule RNA FISH and multiplexed RNA FISH on C. albicans and A. fumigatus
  • you develop imaging analysis pipelines (Phython/R/Matlab) to analyze and quantify single molecule RNA imaging data
  • you develop imaging and quantification approaches to measure the ability of C. albicans and A. fumigatus mRNA localization mutants to infect host cells (e.g. lung epithelial cells)  
  • you communicate your research at local and international conferences 
  • you are actively involved in the research and bioinformatics analysis
  • you publish the results in peer-reviewed journals and a PhD dissertation

Your profile

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that

  • you have a MSc or equivalent degree in Molecular biology, Biophysics, 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 fungal pathogens and mammalian cell cultures 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 do we offer?

The salary will be in accordance with university regulations for academic personnel and amounts €2,770 (PhD) per month during the first year and increases to €3,539 (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 total 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
  • child day-care facilities available on campus
  • optional model for designing a personalized benefits package

Application

Are you interested in this position? Applicants are requested to respond before the deadline: July 15th 2024 at 23:59, via the application button and by uploading the following documents:

  • a letter in which they describe their abilities and motivation
  • a detailed curriculum vitae with two or three references including their emails, phone numbers and their relationship to you
  • a list of grades, TOEFL and/or IETLS scores (applied to non-native English speakers). 
  • If available, a sample of a written report in English
  • Please mention the vacancy number in the header of all your documents.

About us

About the project

Fungi can cause devastating diseases in plants and animals. This is illustrated by the fact that 1.5 million people die each year of a fungal infection, which is higher than caused by malaria or HIV. Infection of humans by the two main human fungal pathogens, Candida albicans and Aspergillus fumigatus, is mediated by their ability to grow by means of elongated cells called hyphae. The tips of these filamentous cells are capable of invading host tissues thereby spreading the infection. Previous studies identified cytoskeleton and vesicle trafficking as important cellular processes to establish and maintain hyphal growth. Interestingly, our teams recently found that also the subcellular localization of RNA molecules within hyphal cells could play a role in their physiology. While the function of sub-cellular localization of mRNAs could not be studied so far due to technological limitations, new tools have recently become available in our labs. Therefore, we are now able for the first time, to study which mRNAs localize at the hyphal tips, how these mRNAs are transported, and whether and how this impacts pathogenicity of C. albicans and A. fumigatus. As a result, we expect to identify novel molecular pathways that are involved in hyphal growth and pathogenicity and that are potential targets for anti-fungal drug therapy. Furthermore, this work has the potential to establish methods and pipelines to investigate other emerging fungal pathogens.

Further particulars

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavour – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.

 Vrije Universiteit Amsterdam is home to more than 26,000 students. We employ over 4,600 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.

The Faculty of Science

The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.

Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Interested

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application.

Submitting a diploma is part of the application process.

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

Your function

Are you looking for a PhD position at the intersection between medical microbiology, fluorescence microscopy and technology development? Do you enjoy developing new methods and performing microscopy, quantitative biology and bioinformatics? The Tutucci group (A-Life & AIMMS, Vrije Universiteit Amsterdam) in Amsterdam, NL is accepting applications for a 4 years fully-funded PhD position starting at the latest on November 1st 2024. Please apply at Vrije Universiteit Amsterdam (VU).

Your duties

  • you develop and perform RNA sequencing on C. albicans and A. fumigatus to identify tip-localized mRNAs
  • you develop and perform single molecule RNA FISH and multiplexed RNA FISH on C. albicans and A. fumigatus
  • you develop imaging analysis pipelines (Phython/R/Matlab) to analyze and quantify single molecule RNA imaging data
  • you develop imaging and quantification approaches to measure the ability of C. albicans and A. fumigatus mRNA localization mutants to infect host cells (e.g. lung epithelial cells)  
  • you communicate your research at local and international conferences 
  • you are actively involved in the research and bioinformatics analysis
  • you publish the results in peer-reviewed journals and a PhD dissertation

Your profile

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that

  • you have a MSc or equivalent degree in Molecular biology, Biophysics, 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 fungal pathogens and mammalian cell cultures 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 do we offer?

The salary will be in accordance with university regulations for academic personnel and amounts €2,770 (PhD) per month during the first year and increases to €3,539 (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 total 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
  • child day-care facilities available on campus
  • optional model for designing a personalized benefits package

Application

Are you interested in this position? Applicants are requested to respond before the deadline: July 15th 2024 at 23:59, via the application button and by uploading the following documents:

  • a letter in which they describe their abilities and motivation
  • a detailed curriculum vitae with two or three references including their emails, phone numbers and their relationship to you
  • a list of grades, TOEFL and/or IETLS scores (applied to non-native English speakers). 
  • If available, a sample of a written report in English
  • Please mention the vacancy number in the header of all your documents.

About us

About the project

Fungi can cause devastating diseases in plants and animals. This is illustrated by the fact that 1.5 million people die each year of a fungal infection, which is higher than caused by malaria or HIV. Infection of humans by the two main human fungal pathogens, Candida albicans and Aspergillus fumigatus, is mediated by their ability to grow by means of elongated cells called hyphae. The tips of these filamentous cells are capable of invading host tissues thereby spreading the infection. Previous studies identified cytoskeleton and vesicle trafficking as important cellular processes to establish and maintain hyphal growth. Interestingly, our teams recently found that also the subcellular localization of RNA molecules within hyphal cells could play a role in their physiology. While the function of sub-cellular localization of mRNAs could not be studied so far due to technological limitations, new tools have recently become available in our labs. Therefore, we are now able for the first time, to study which mRNAs localize at the hyphal tips, how these mRNAs are transported, and whether and how this impacts pathogenicity of C. albicans and A. fumigatus. As a result, we expect to identify novel molecular pathways that are involved in hyphal growth and pathogenicity and that are potential targets for anti-fungal drug therapy. Furthermore, this work has the potential to establish methods and pipelines to investigate other emerging fungal pathogens.

Further particulars

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavour – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.

 Vrije Universiteit Amsterdam is home to more than 26,000 students. We employ over 4,600 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.

The Faculty of Science

The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.

Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Questions about the vacancy?

Please contact

Evelina Tutucci

Assistant Professor

Interested

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application.

Submitting a diploma is part of the application process.

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

Questions about the vacancy?

Please contact

Evelina Tutucci

Assistant Professor

Application procedure

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